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<h3>
Nilesh Patra pushed to branch debian/master
at <a href="https://salsa.debian.org/med-team/dcm2niix">Debian Med / dcm2niix</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/dcm2niix/-/commit/dfc52f1a99506f9fb80724fcadd96ff3b83e5477">dfc52f1a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-24T14:11:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.20210317</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dcm2niix/-/commit/a0c727941286053cb36e9c6cc2cb22c69ac22932">a0c72794</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-24T14:11:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dcm2niix/-/commit/03a4908dd65be1cef2704b4ffbefc2071ad7f7c1">03a4908d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-24T14:11:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.0.20210317'
Update to upstream version '1.0.20210317'
with Debian dir 460f8362939deac5da9e93c11481525e9488474a</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dcm2niix/-/commit/06e79733408f004fd9d7554feaf4d8049c5d7158">06e79733</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-24T14:11:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
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<h4>19 changed files:</h4>
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<a href="#a03585ab89eed5e0782a1875b2d8153b97865d30">
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.github/ISSUE_TEMPLATE/bug_report.md
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#124278c26ad74cc9b1858d5773e307a0f809b2e0">
Canon/README.md
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<li class="file-stats">
<a href="#f979519797b71359a5e657a3ffdd75de78a54907">
FILENAMING.md
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<li class="file-stats">
<a href="#21100b265d604a6fd4bef7d79287c7d6070503d3">
GE/README.md
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<li class="file-stats">
<a href="#c043db414dbc8caf6a5d997e1c8015749a800b2b">
Philips/README.md
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#8695819d77758369f3264b90f25fdd66b2231dde">
UIH/README.md
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<a href="#d19bcb068e96ecf84a2a5f6708a2d78f166177ff">
console/CMakeLists.txt
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<a href="#6161009529e5e4e6364b2f49e592dc6ea75e4594">
console/main_console.cpp
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<a href="#5960b99778897bf78ce0e20de3260a5c26016eec">
console/nifti1_io_core.cpp
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<a href="#966be9a60ccbbd15be352c99c24de65122ff7e63">
console/nifti1_io_core.h
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<a href="#7f920a885f04d331121e6efbfd08cb9080cb5038">
console/nii_dicom.cpp
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<a href="#dec6a857028e619f96c0e3ba3e43dfdc5bce1b7f">
console/nii_dicom.h
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<a href="#ef8e48ac088b20316ce9b8a7853d81ba9b64f51b">
console/nii_dicom_batch.cpp
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console/nii_dicom_batch.h
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console/notarize.sh
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<h4>Changes:</h4>
<li id="a03585ab89eed5e0782a1875b2d8153b97865d30">
<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#a03585ab89eed5e0782a1875b2d8153b97865d30"><strong>.github/ISSUE_TEMPLATE/bug_report.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bug report</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="na" style="color: #008080;">about</span><span class="pi">:</span> <span class="s" style="color: #d14;">Create a report to help us improve</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="na" style="color: #008080;">title</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="na" style="color: #008080;">labels</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="na" style="color: #008080;">assignees</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Describe the bug**</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">A clear and concise description of what the bug is.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**To Reproduce**</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">Steps to reproduce the behavior:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">1.</span> Run the command 'dcm2niix ...'</span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">2.</span> See error ...</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Expected behavior**</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">A clear and concise description of what you expected to happen.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Output Log**</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">If applicable, output generated converting data.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">** Version (please complete the following information):**</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p"> -</span> dcm2niix version string, e.g. <span class="sb" style="color: #d14;">`dcm2niiX version v1.0.20201207 Clang12.0.0 ARM (64-bit MacOS)`</span> The version string is always the first line generated when dcm2niix is run.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p"> -</span> Is this the <span class="p">[</span><span class="nv" style="color: #008080;">latest stable release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rordenlab/dcm2niix/releases</span><span class="p">)</span>? If not, does the latest stable release resolve your issue?</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p"> -</span> If the latest stable version fails, and you are using Windows. Does the latest commit on the development branch resolve your issue? You can get a pre-compiled version from <span class="p">[</span><span class="nv" style="color: #008080;">AppVeyor</span><span class="p">](</span><span class="sx" style="color: #d14;">https://ci.appveyor.com/project/neurolabusc/dcm2niix</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">click</span> on the Artifacts button).</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p"> -</span> If the latest stable version fails, and you are using macOS or Linux. Does the latest commit on the development branch resolve your issue? You can build this using the recipe below:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown">git clone --branch development https://github.com/rordenlab/dcm2niix.git</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">cd dcm2niix/console</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">g++ -I. main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">./dcm2niix ....</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">```</span></span></pre>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,9 +22,7 @@ matrix:</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${MATRIX_EVAL}"</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git submodule update --init --depth=3 dcm_qa</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git submodule update --init --depth=3 dcm_qa_nih</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git submodule update --init --depth=3 dcm_qa_uih</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git submodule update --init --remote --depth=3</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># - mkdir build && cd build && cmake -DBATCH_VERSION=ON -DUSE_OPENJPEG=ON -DUSE_JPEGLS=true -DZLIB_IMPLEMENTATION=Cloudflare .. && make && cd -</span></span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#124278c26ad74cc9b1858d5773e307a0f809b2e0"><strong>Canon/README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">dcm2niix can convert Canon (né Toshiba) DICOM format images to NIfTI. This page notes vendor specific conversion details.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Avoid Classic DICOM</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">Users of Canon MRI equipment are strongly advised to export data from their scanners as enhanced DICOM (with all images from the series stored as a single file) rather than classic DICOM (each 2D slice stored as a separate file). Limitations of the Canon classic DICOMs are described <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rordenlab/dcm2niix/issues/495</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/neurolabusc/dcm_qa_canon</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Diffusion Weighted Imaging Notes</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown">In contrast to several other vendors, Toshiba used public tags to report diffusion properties. Specifically, <span class="p">[</span><span class="nv" style="color: #008080;">DiffusionBValue (0018,9087)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,9087</span><span class="p">)</span>) and <span class="p">[</span><span class="nv" style="color: #008080;">DiffusionGradientOrientation (0018,9089)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,9089</span><span class="p">)</span>). Be aware that these tags are only populated for images where a diffusion gradient is applied. Consider a typical diffusion series where some volumes are acquired with B=0 while others have B=1000. In this case, only the volumes with B>0 will report a DiffusionBValue.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">In contrast to several other vendors, Toshiba used public tags to report diffusion properties. Specifically, <span class="p">[</span><span class="nv" style="color: #008080;">DiffusionBValue (0018,9087)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,9087</span><span class="p">)</span>) and <span class="p">[</span><span class="nv" style="color: #008080;">DiffusionGradientOrientation (0018,9089)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,9089</span><span class="p">)</span>). Be aware that these tags are only populated for images where a diffusion gradient is applied. Consider a typical diffusion series where some volumes are acquired with B=0 while others have B=1000. In this case, only the volumes with B>0 will report a DiffusionBValue.<span class="idiff left right"> These coordinates are with respect to the scanner bore, not image space.</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">Since the acquisition by Canon, these public tags are no longer populated. The diffusion gradient directions are now stored in the ASCII Image Comments tag. Like GE (but unlike <span class="p">[</span><span class="nv" style="color: #008080;">Siemens, GE and Toshiba</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.na-mic.org/wiki/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI</span><span class="p">)</span>), these directions are with respect to the image space, not the scanner bore. F<span class="idiff left">or empirical data see the Sample Dat</span>ase<span class="idiff">ts</span> se<span class="idiff right">ction.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">Since the acquisition by Canon, these public tags are no longer populated<span class="idiff left"> for images saved in classic 2D DICOM format</span>. The diffusion gradient directions are now stored in the ASCII Image Comments tag. Like GE (but unlike <span class="p">[</span><span class="nv" style="color: #008080;">Siemens, GE and Toshiba</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.na-mic.org/wiki/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI</span><span class="p">)</span>), these directions are with respect to the image space, not the scanner bore. F<span class="idiff">urther, gradient direction is not adjusted for phase encoding polarity, and it is impossible to determine phase encoding polarity. For detailed discussion and a validation dataset that exhibits these attributes ple</span>ase se<span class="idiff">e </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">dcm_qa_canon</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/neurolabusc/dcm_qa_canon</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">. A Canon classic DICOM DWI image may report:</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"> (0018,9087) FD 1500 # 8, 1 DiffusionBValue</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"> (0020,4000) LT [b=1500(0.445,0.000,0.895)] # 26, 1 ImageComments</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="p">```</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown">In contrast, when exporting images as enhanced (4D) DICOM, information is stored in public tags and does appear to compensate for phase encode polarity. These coordinates are with respect to the scanner bore, not image space. A Canon classic DICOM DWI image may report: </span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown">(0018,9087) FD 1500 # 8, 1 DiffusionBValue</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">(0018,9089) FD 0.29387456178665161\-0.95365142822265625\-0.064700603485107422 # 24, 3 DiffusionGradientOrientation</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Unknown Properties</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<li id="f979519797b71359a5e657a3ffdd75de78a54907">
<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#f979519797b71359a5e657a3ffdd75de78a54907"><strong>FILENAMING.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,6 +12,7 @@ You request the output file name with the `-f` argument. For example, consider y</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p"> -</span> %d=description (from 0008,103E)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p"> -</span> %e=echo number (from 0018,0086)</span>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="p"> -</span> %f=folder name (name of folder containing first DICOM)</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p"> -</span> %g=accession number (0008,0050)</span>
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15
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p"> -</span> %i=ID of patient (from 0010,0020)</span>
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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="p"> -</span> %j=series instance UID (from 0020,000E)</span>
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17
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="p"> -</span> %k=study instance UID (from 0020,000D)</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +20,7 @@ You request the output file name with the `-f` argument. For example, consider y</td>
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19
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p"> -</span> %m=manufacturer short name (from 0008,0070: GE, Ph, Si, To, UI, NA)</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p"> -</span> %n=name of patient (from 0010,0010)</span>
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21
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p"> -</span> %o=mediaObjectInstanceUID (0002,0003)<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="p"> -</span> %p=protocol name (from 0018,1030). If 0018,1030 is empty, <span class="idiff left">or if the Manufacturer (0008,0070) is GE with Modality (0008,0060) of MR, then </span>the SequenceName (0018,0024) is used<span class="idiff right"> if it is not empty</span>.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p"> -</span> %p=protocol name (from 0018,1030). If 0018,1030 is empty, the SequenceName (0018,0024) is used.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p"> -</span> %r=instance number (from 0020,0013)<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="p"> -</span> %s=series number (from 0020,0011)</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="p"> -</span> %t=time of study (from 0008,0020 and 0008,0030)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,6 +50,7 @@ In general dcm2niix creates images with 3D dimensions, or 4 dimensions when the</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown">Some post-fixes are specific to Philips DICOMs</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"><span class="p"> -</span> _ADC Philips specific case. A DWI image where derived isotropic, ADC or trace volume was appended to the series. Since this image will disrupt subsequent processing, and because subsequent processing (dwidenoise, topup, eddy) will yield better derived images, dcm2niix will also create an additional image without this volume. Therefore, the _ADC file should typically be discarded. If you want dcm2niix to discard these useless derived images, use the ignore feature ('-i y').</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="p"> -</span> _fieldmaphz unwrapped B0 field map (in Hz) generated by a Philips scanner. Suggests Image Type (0008,0008) includes the terms 'B0' and 'MAP'.</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="p"> -</span> _Raw Philips XX_<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> DICOMs (Raw Data Storage).</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"><span class="p"> -</span> _PS Philips PS_<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> DICOMs (Grayscale Softcopy Presentation State).</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,9 +69,9 @@ dcm2niix will attempt to write your image using the naming scheme you specify wi</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Special Characters</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Some characters are not permitted</span><span class="p">](</span><span class="sx" style="color: #d14;">https://stackoverflow.com/questions/1976007/what-characters-are-forbidden-in-windows-and-linux-directory-names</span><span class="p">)</span> in file names. The following characters will be replaced with underscorces (<span class="sb" style="color: #d14;">`_`</span>). Note that the forbidden characters vary between operating systems (Linux only forbids the forward slash, MacOS forbids forward slash and colon, while Windows forbids any of the characters listed below). To ensure that files can be easily copied between file systems, <span class="p">[</span><span class="nv" style="color: #008080;">dcm2niix restricts file names to characters allowed by Windows</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rordenlab/dcm2niix/issues/237</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Some characters are not permitted</span><span class="p">](</span><span class="sx" style="color: #d14;">https://stackoverflow.com/questions/1976007/what-characters-are-forbidden-in-windows-and-linux-directory-names</span><span class="p">)</span> in file names. The following characters will be replaced with underscorces (<span class="sb" style="color: #d14;">`_`</span>). Note that the forbidden characters vary between operating systems (Linux only forbids the forward slash, MacOS forbids forward slash and colon, while Windows forbids any of the characters listed below). To ensure that files can be easily copied between file systems, <span class="p">[</span><span class="nv" style="color: #008080;">dcm2niix restricts file names to characters allowed by Windows</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rordenlab/dcm2niix/issues/237</span><span class="p">)</span>.<span class="idiff left"> While technically legal in all filesystems, the semicolon can wreak havoc in </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Windows</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://stackoverflow.com/questions/3869594/semi-colons-in-windows-filenames</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> and </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Linux</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://forums.plex.tv/t/linux-hates-semicolons-in-file-names/49098/2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">. </span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### List of Forbidden Characters<span class="idiff left right"> (based on Windows)</span></span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### List of Forbidden Characters</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown">< (less than)</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown">> (greater than)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,6 +82,7 @@ dcm2niix will attempt to write your image using the naming scheme you specify wi</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown">| (vertical bar or pipe)</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown">? (question mark)</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">* (asterisk)</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown">; (semicolon) </span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Control characters</span><span class="p">](</span><span class="sx" style="color: #d14;">https://en.wikipedia.org/wiki/ASCII#Control_characters</span><span class="p">)</span> like backspace and tab are also forbidden.</span>
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<li id="21100b265d604a6fd4bef7d79287c7d6070503d3">
<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#21100b265d604a6fd4bef7d79287c7d6070503d3"><strong>GE/README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,7 +34,29 @@ Some sequences allow the user to interpolate images in plane (e.g. saving a 2D 6</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Total Readout Time</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown">One often wants to determine <span class="p">[</span><span class="nv" style="color: #008080;">echo spacing, bandwidth</span><span class="p">](</span><span class="sx" style="color: #d14;">https://support.brainvoyager.com/brainvoyager/functional-analysis-preparation/29-pre-processing/78-epi-distortion-correction-echo-spacing-and-bandwidth</span><span class="p">)</span> and total read-out time for EPI data so they can be undistorted. Total readout time is influenced by parallel acceleration factor, bandwidth, number of EPI lines, and partial Fourier. Not all of these parameters are available from the GE DICOM images, so a user needs to check the scanner console.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown">One often wants to determine <span class="p">[</span><span class="nv" style="color: #008080;">echo spacing, bandwidth</span><span class="p">](</span><span class="sx" style="color: #d14;">https://support.brainvoyager.com/brainvoyager/functional-analysis-preparation/29-pre-processing/78-epi-distortion-correction-echo-spacing-and-bandwidth</span><span class="p">)</span> and total read-out time for EPI data so they can be undistorted. Specifically, we are interested in FSL's definition of total read-out time, which may differ from the actual read-out time. FSL expects “the time from the middle of the first echo to the middle of the last echo, as it would have been had partial k-space not been used”. So total read-out time is influenced by parallel acceleration factor, bandwidth, number of EPI lines, but not partial Fourier. For GE data we can use the Acquisition Matrix (0018,1310) in the phase-encoding direction, the in-plane acceleration ASSET R factor (the reciprocal of this is stored as the first element of 0043,1083) and the Effective Echo Spacing (0043,102C). While GE does not tell us the <span class="p">[</span><span class="nv" style="color: #008080;">partial Fourier fraction</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html</span><span class="p">)</span>, is does reveal if it is present with the ScanOptions (0018,1022) reporting <span class="p">[</span><span class="nv" style="color: #008080;">PFF</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Ttable&q=C.8-4</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">in</span> my experience, GE does not populate <span class="p">[</span><span class="nv" style="color: #008080;">(0018,9081)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,9081</span><span class="p">)</span>)). While partial Fourier does not impact FSL's totalReadoutTime directly, it can interact with the number of lines acquired when combined with parallel imaging (the <span class="sb" style="color: #d14;">`Round_factor`</span> 2 (Full Fourier) or 4 (Partial Fourier)).</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown">The formula for FSL's definition of TotalReadoutTime (in seconds) is:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">TotalReadoutTime = ( ( ceil ((1/Round_factor) * PE_AcquisitionMatrix / Asset_R_factor ) * Round_factor) - 1 ] * EchoSpacing * 0.000001</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown">EffectiveEchoSpacing = TotalReadoutTime/ (reconMatrixPE - 1)</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown">Consider an example:</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown">(0018,1310) US 128\0\0\128 # 8, 4 AcquisitionMatrix</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">(0018,0022) CS [SAT_GEMS\MP_GEMS\EPI_GEMS\ACC_GEMS\PFF\FS] # 42, 6 ScanOptions</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown">(0043,102c) SS 636 # 2, 1 EchoSpacing</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown">(0043,1083) DS [0.666667\1] # 10, 2 Acceleration</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">From this we can derive:</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">ASSET= 1.5 PE_AcquisitionMatrix= 128 EchoSpacing= 636 Round_Factor= 4 TotalReadoutTime= 0.055332</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Image Acceleration</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,6 +64,10 @@ The BIDS [ParallelReductionFactorInPlane](https://bids-specification.readthedocs</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown">The BIDS <span class="p">[</span><span class="nv" style="color: #008080;">MultibandAccelerationFactor</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#rf-contrast</span><span class="p">)</span> can be determined from the private tag <span class="sb" style="color: #d14;">`Multiband Parameters`</span> (0043,10B6). This is an array with at least three values, the first is the Multiband (aka HyperBand) factor, the second is the Slice FOV Shift Factor, and the final is the Calibration method. For example, a scan using a multiband factor of 2 could be reported as <span class="sb" style="color: #d14;">`(0043,10b6) LO [2\4\19\\\\]`</span>. </span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Missing Information</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown">While GE DICOMs will report if the image uses partial Fourier, it will not reveal the partial Fourier fraction.</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Phase-Encoding Polarity</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown">All EPI scans have spatial distortion, particularly those with longer readout times. Tools like <span class="p">[</span><span class="nv" style="color: #008080;">FSL topup</span><span class="p">](</span><span class="sx" style="color: #d14;">https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide</span><span class="p">)</span> can leverage data where two spin-echo images are acquired that are identical except for using opposite phase-encoding polarity (e.g. one uses A>P, the other P>A). Each image is distorted with the same magnitude, but in the opposite direction. GE's Rx27 software version and later populate the <span class="p">[</span><span class="nv" style="color: #008080;">Rectilinear Phase Encode Reordering (0018,9034)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,9034</span><span class="p">)</span>) tag which for EPI is set to either LINEAR or REVERSE_LINEAR.</span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#c043db414dbc8caf6a5d997e1c8015749a800b2b"><strong>Philips/README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## About</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown">dcm2niix attempts to convert all DICOM images to NIfTI. The Philips enhanced DICOM images are elegantly able to save all images from a series as a single file. However, this format is necessarily complex. The usage of this format has evolved over time, and can become further complicated when DICOM are <span class="idiff left">handl</span>ed by DICOM tools (for example, anonymization, <span class="idiff right">transfer which converts</span> explicit VRs to implicit VRs, etc.).</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">dcm2niix attempts to convert all DICOM images to NIfTI. The Philips enhanced DICOM images are elegantly able to save all images from a series as a single file. However, this format is necessarily complex. The usage of this format has evolved over time, and can become further complicated when DICOM are <span class="idiff left">modifi</span>ed by DICOM tools (for example, anonymization, <span class="idiff">mangled by a </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">dcm4che/AGFA PACS</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/neurolabusc/dcm_qa_agfa</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">, conversion of</span> explicit VRs to implicit VRs, etc.).</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">This web page describes some of the strategies handle these images. However, users should be vigilant when handling these datasets. If you encounter problems using dcm2niix you can explore <span class="p">[</span><span class="nv" style="color: #008080;">alternative DICOM to NIfTI converters</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Alternatives</span><span class="p">)</span> or <span class="p">[</span><span class="nv" style="color: #008080;">report an issue</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rordenlab/dcm2niix</span><span class="p">)</span>.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,24 +18,62 @@ Therefore, dcm2niix will ignore the IPP enclosed in 2005,140F unless no alternat</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Image Scaling</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="idiff left">dcm2niix losslessy copies the raw data from DICOM to NIfTI format. These values are typically stored as 16-bit integers in the range -32768..32767. Both the DICOM and NIfTI formats describe how scaling intercept and slope</span> values <span class="idiff">can</span> be use<span class="idiff right">d to convert these raw values into calibrated values. For example, with an intercept of 0 and slope of 0.01 the raw value of 50 would be converted to 0.5. </span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="idiff left">How data is represented in DICOM for MR has several challenges and the technology and standard has evolved over the years to accommodate new uses. Unlike CT, where the signal is naturally displayed in Hounsfield units, MR has no natural signal units and the magnitude is influenced by the electronics and the software processing required to bring this to the final image. Secondly most of the original DICOM implementations used small bit number integers to store the underlying images for economy of storage. As a result it is necessary to apply scaling from the internal DICOM storage to a form suitable for radiographic display or quantitative measurement. There remain several challenges with this process, ensuring that the mapping to the integer</span> values <span class="idiff">makes</span> be<span class="idiff">st</span> use<span class="idiff right"> of the available bit depth for images with large dynamic range, or large changes between images, without clipping the data while also preserving the appearance of the noise field which is demanded by the needs of radiographic visual review. Note that for most MRI modalities these concerns do not impact analyses: the intensity is assumed arbitrary, the statistics treat signal offset and scaling as nuisance regressors when fitting models, and cacluations are computed with high precision floating point numbers. However, there are some situations such as arterial spin labeling where image scaling is important. In these situations, scaling is a crucial aspect to be aware of for quantitative methods and which representation is used depends upon your needs.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="idiff left">Unlike other vendors, Philips can store different scaling factors in their DICOM header. For most MRI modalities where the intensity brightness is relative, this has no impact. However, for modalities like ASL it can have an impact. The NIfTI format requires a single intensity intercept and slope is chosen. Therefore, dcm2niix will choose the "Real World" values if provided. If these are not available, dcm2niix will choose either the "precise" (default) or "display" (if the user choose "-p n") value. dcm2niix will also populate the folllowing</span> tags in the <span class="idiff right">BIDS header that allow the user to select between different intensity scaling formats: "PhilipsRescaleSlope", "PhilipsRescaleIntercept", "PhilipsScaleSlope", "UsePhilipsFloatNotDisplayScaling" (where "1" indicates NIfTI uses precise value, and "0" indicates display values)., "PhilipsRWVSlope" and "PhilipsRWVIntercept"</span>.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="idiff left">At its simplest image scaling requires a rescale slope and intercept defined by the DICOM standard tags </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">0028,1053</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0028,1053</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">) and </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">0028,1052</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0028,1053</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">). Whether these values are the same for all images, or image specific depends upon the implementation and potentially the location of these</span> tags <span class="idiff">with</span>in<span class="idiff">g</span> the <span class="idiff right">DICOM tag structure. For manufacturers other than Philips, these are the only intensity scaling values provided, so there is no concern regarding which scaling values should be used</span>.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">The relevant DICOM tags are</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown">RS = rescale slope (<span class="p">[</span><span class="nv" style="color: #008080;">0028,1053</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0028,1053</span><span class="p">)</span>))</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown">RI = rescale intercept (<span class="p">[</span><span class="nv" style="color: #008080;">0028,1052</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0028,1052</span><span class="p">)</span>))</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown">SS = scale slope (2005,100E)</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">RealWorldIntercept = (0040,9224) </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown">Real World Slope = (0040,9225)</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown">The transformation formulas are:</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">R = raw value, P = precise value, D = displayed value</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">D = R <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> RS + RI</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown">P = D/(RS <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> SS)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">However, the DICOM standard introduced the concept of <span class="p">[</span><span class="nv" style="color: #008080;">`real world units`</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dicom.nema.org/dicom/2013/output/chtml/part03/sect_A.46.html</span><span class="p">)</span>. This allows the storage of one or more mappings to allow selective viewing of the data mapped into different value ranges (which may also be non-linear mappings).</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">Philips thinks in terms of three different representations (using the terminology of the documentation available to Philips collaborators):</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">| Name | ID | Description|</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">| ---------------- | ------------- | ------------- |</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown">| Stored Value | SV | Raw data stored in DICOM tag PIXEL DATA tag (7FE0,0010)|</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">| Displayed Value | DV | The value which is shown to the user when using scanner interface, ROIS, measurements etc. |</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">| Floating Point | FP | An internal value at a point earlier in the reconstruction chain before the conversion to DICOM/integer for image presentation. |</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">| Real World Value | WV | DICOM defined real world units|</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">In general SV should not be used for quantitative measurements as it is an integer format. In practice, if the Rescale values are the same for all images (the typical case, but not guaranteed) SV can be used to compare signal intensities between images from the same scan. Note that the NIfTI format only provides a single <span class="sb" style="color: #d14;">`scl_slope`</span> and <span class="sb" style="color: #d14;">`scl_inter`</span> for the entire file, whereas in DICOM rescale values can in theory differ across 2D slices. Therefore, in situations where the rescale values do differ across slices, dcm2niix will apply the requested rescale to each slice and save the scaled data as the 32-bit float NIfTI dataset. This preserves the varibility reported by the rescale tags, at the cost of disk space. </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown">DV can be used for quantitative comparison of signal intensities between images in the same scan as long as the relevant rescale values are taken into account. These rescale values may come from the tags standard tags 0028,1053 and 0028,1052 or from a relevant RealWorld block if present. If the DV is derived from a RealWorld block with defined units (tag (0008,0104) such as Hz or ms rather than “no units”) or a RescaleType (0028,1054) with a non-US type (not defined by the standard), then the DV is already quantitative and cross scan comparison may be done.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown">However, in general DV is not sufficient to compare images from different scans, especially if the signal intensity varies a lot (eg multiple inversion recovery scans) in which case the FP value may be used as this may be compared (with some caveats) across scans and across timescales. This scaling requires an additional scale factor on top of the DV value, the Scale Slope (private tag (2005,100E))</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">As long as rescale values are identical across all DICOM slices, dcm2niix losslessly copies the raw pixel data from the DICOM tag (7FE0,0010) to NIfTI image. These values are typically stored as 16-bit integers in the range -32768..32767. Both the DICOM and NIfTI formats describe how scaling intercept and slope values can be used to convert these raw values into calibrated values. For example, with an intercept of 0 and slope of 0.01 the raw value of 50 would be converted to 0.5. </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown">The <span class="p">[</span><span class="nv" style="color: #008080;">NIfTI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h</span><span class="p">)</span> header provides the <span class="sb" style="color: #d14;">`scl_slope`</span> and <span class="sb" style="color: #d14;">`scl_inter`</span> fields so each voxel value in the dataset is scaled as:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown">I = scl_slope * SV + scl_inter</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">where <span class="sb" style="color: #d14;">`SV`</span> is the raw stored value and <span class="sb" style="color: #d14;">`I`</span> is the "true" transformed voxel intensity.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown">Philips has three possible intensity transforms for their DICOM images (world (<span class="sb" style="color: #d14;">`W`</span>), display (<span class="sb" style="color: #d14;">`D`</span>), precise (<span class="sb" style="color: #d14;">`P`</span>)). All of these transforms might be provided in a single DICOM image, while the <span class="p">[</span><span class="nv" style="color: #008080;">NIfTI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h</span><span class="p">)</span> header only designates a single <span class="sb" style="color: #d14;">`scl_slope`</span> and <span class="sb" style="color: #d14;">`scl_inter`</span> for each image. dcm2niix will attempt to retain the stored values (<span class="sb" style="color: #d14;">`SV`</span>) and sets the NIfTI <span class="sb" style="color: #d14;">`scl_inter`</span> and <span class="sb" style="color: #d14;">`scl_slope values`</span> for the desired intensity transform. dcm2niix will use <span class="sb" style="color: #d14;">`FP`</span> if possible. If this is not possibleor the user specifies <span class="sb" style="color: #d14;">`-p n`</span> dcm2niix will use the transforms for <span class="sb" style="color: #d14;">`DV`</span>.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown">The formulas are provided below. The DICOM tags are in brackets (e.g. <span class="sb" style="color: #d14;">`(0040,9225)`</span>) and the BIDS tag is in double quotes (e.g. <span class="sb" style="color: #d14;">`"PhilipsRWVSlope"`</span>). Since all the scaling values are stored in the BIDS sidecar, you can always use these to later your preferred intensity transform (assume all slices used the same scaling values).</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">Inputs:</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"> SV = stored value of DICOM PIXEL DATA without scaling</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"> WS = RealWorldValue slope (0040,9225) "PhilipsRWVSlope"</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"> WI = RealWorldValue intercept (0040,9224) "PhilipsRWVIntercept"</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"> RS = rescale slope (0028,1053) "PhilipsRescaleSlope"</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"> RI = rescale intercept (0028,1052) "PhilipsRescaleIntercept"</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"> SS = scale slope (2005,100E) "PhilipsScaleSlope"</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">Outputs:</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"> WV = real world value</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"> FP = precise value</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"> DV = displayed value</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown">Formulas:</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"> WV = SV * WS + WI</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"> DV = SV * RS + RI</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"> FP = DV / (RS * SS)</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Derived parametric maps stored with raw diffusion data</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown">Some Philips diffusion DICOM images include derived image(s) along with the images. Other manufacturers save these derived images as a separate series number, and the DICOM standard seems ambiguous on whether it is allowable to mix raw and derived data in the same series (see PS 3.3-2008, C.7.6.1.1.2-3). In practice, many Philips diffusion images append <span class="p">[</span><span class="nv" style="color: #008080;">derived parametric maps</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.revisemri.com/blog/2008/diffusion-tensor-imaging/</span><span class="p">)</span> with the original data. With Philips, appending the derived isotropic image is optional <span class="idiff left"> </span>- it is only created for the 'clinical' DTI schemes for radiography analysis and is triggered if the first three vectors in the gradient table are the unit X,Y and Z vectors. For conventional DWI, the result is the conventional mean of the ADC <span class="idiff right"> </span>X,Y,Z for DTI it the conventional mean of the 3 principle Eigen vectors. As scientists, we want to discard these derived images, as they will disrupt data processing and we can generate better parametric maps after we have applied undistortion methods such as <span class="p">[</span><span class="nv" style="color: #008080;">Eddy and Topup</span><span class="p">](</span><span class="sx" style="color: #d14;">https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide</span><span class="p">)</span>. The current version of dcm2niix uses the Diffusion Directionality (0018,9075) tag to detect B=0 unweighted ("NONE"), B-weighted ("DIRECTIONAL"), and derived ("ISOTROPIC") images. Note that the Dimension Index Values (0020,9157) tag provides an alternative approach to discriminate these images. Here are sample tags from a Philips enhanced image that includes and derived map (3rd dimension is "1" while the other images set this to "2").</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown">Some Philips diffusion DICOM images include derived image(s) along with the images. Other manufacturers save these derived images as a separate series number, and the DICOM standard seems ambiguous on whether it is allowable to mix raw and derived data in the same series (see PS 3.3-2008, C.7.6.1.1.2-3). In practice, many Philips diffusion images append <span class="p">[</span><span class="nv" style="color: #008080;">derived parametric maps</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.revisemri.com/blog/2008/diffusion-tensor-imaging/</span><span class="p">)</span> with the original data. With Philips, appending the derived isotropic image is optional - it is only created for the 'clinical' DTI schemes for radiography analysis and is triggered if the first three vectors in the gradient table are the unit X,Y and Z vectors. For conventional DWI, the result is the conventional mean of the ADC X,Y,Z for DTI it the conventional mean of the 3 principle Eigen vectors. As scientists, we want to discard these derived images, as they will disrupt data processing and we can generate better parametric maps after we have applied undistortion methods such as <span class="p">[</span><span class="nv" style="color: #008080;">Eddy and Topup</span><span class="p">](</span><span class="sx" style="color: #d14;">https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide</span><span class="p">)</span>. The current version of dcm2niix uses the Diffusion Directionality (0018,9075) tag to detect B=0 unweighted ("NONE"), B-weighted ("DIRECTIONAL"), and derived ("ISOTROPIC") images. Note that the Dimension Index Values (0020,9157) tag provides an alternative approach to discriminate these images. Here are sample tags from a Philips enhanced image that includes and derived map (3rd dimension is "1" while the other images set this to "2").</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown">(0018,9075) CS [DIRECTIONAL]</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +140,7 @@ Another value desirable for TOPUP is the "TotalReadoutTime". Again, one can not</td>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Partial Volumes</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="markdown">NIfTI expects all 3D volumes of a <span class="idiff left right"> </span>4D series to have the same number of series (e.g. a time series of 3D fMRI volumes, or a diffusion set with 3D volumes with different gradients applied). If a fMRI sequence is aborted part way through, it is possible that a Philips scanner will only save part of the final volume. An example would be where the total slices (9970) does not equal Dynamics (290) x slices (35) = 10150. Current versions of dcm2niix expect complete volumes. You can repair your data using the console or a Python script, as discussed in <span class="p">[</span><span class="nv" style="color: #008080;">issue 357</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rordenlab/dcm2niix/issues/357</span><span class="p">)</span>. To resolve this situation by hand you could also <span class="p">[</span><span class="nv" style="color: #008080;">rename</span><span class="p">](</span><span class="sx" style="color: #d14;">RENAMING.md</span><span class="p">)</span> your DICOM files with a call like <span class="sb" style="color: #d14;">`./dcm2niix -r y -f %t/%s_%p_%4y_%2r.dcm ~/out 0020,0100`</span>. In this example, the <span class="p">[</span><span class="nv" style="color: #008080;">`%4y`</span><span class="p">](</span><span class="sx" style="color: #d14;">FILENAMING.md</span><span class="p">)</span> parameter adds the volume (Temporal Position, 0020,0100) to the filename, allowing you to identify volumes with missing slices.</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown">NIfTI expects all 3D volumes of a 4D series to have the same number of series (e.g. a time series of 3D fMRI volumes, or a diffusion set with 3D volumes with different gradients applied). If a fMRI sequence is aborted part way through, it is possible that a Philips scanner will only save part of the final volume. An example would be where the total slices (9970) does not equal Dynamics (290) x slices (35) = 10150. Current versions of dcm2niix expect complete volumes. You can repair your data using the console or a Python script, as discussed in <span class="p">[</span><span class="nv" style="color: #008080;">issue 357</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rordenlab/dcm2niix/issues/357</span><span class="p">)</span>. To resolve this situation by hand you could also <span class="p">[</span><span class="nv" style="color: #008080;">rename</span><span class="p">](</span><span class="sx" style="color: #d14;">RENAMING.md</span><span class="p">)</span> your DICOM files with a call like <span class="sb" style="color: #d14;">`./dcm2niix -r y -f %t/%s_%p_%4y_%2r.dcm ~/out 0020,0100`</span>. In this example, the <span class="p">[</span><span class="nv" style="color: #008080;">`%4y`</span><span class="p">](</span><span class="sx" style="color: #d14;">FILENAMING.md</span><span class="p">)</span> parameter adds the volume (Temporal Position, 0020,0100) to the filename, allowing you to identify volumes with missing slices.</span>
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106
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Non-Image DICOMs</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -125,5 +163,8 @@ Prior versions of dcm2niix used different methods to sort images. However, these</td>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Sample Datasets</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">National Alliance for Medical Image Computing (NAMIC) samples</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.insight-journal.org/midas/collection/view/194</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Unusual Philips Examples</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Unusual_MRI</span><span class="p">)</span>.</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Diffusion Examples</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging</span><span class="p">)</span>.</span></pre>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Unusual Philips Examples (e.g. multi-echo)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Unusual_MRI</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Archival samples</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Archival_MRI</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Diffusion Examples</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Additional Diffusion Examples</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/neurolabusc/dcm_qa_philips</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Enhanced DICOMs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/neurolabusc/dcm_qa_enh</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,6 +40,7 @@ There are a couple ways to install dcm2niix</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="p"> -</span> Run the following command to get the latest version for Linux, Macintosh or Windows: </span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip`</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_mac.zip`</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_mac_arm.pkg`</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_win.zip`</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">MRIcroGL (NITRC)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nitrc.org/projects/mricrogl</span><span class="p">)</span> or <span class="p">[</span><span class="nv" style="color: #008080;">MRIcroGL (GitHub)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rordenlab/MRIcroGL12/releases</span><span class="p">)</span> includes dcm2niix that can be run from the command line or from the graphical user interface (select the Import menu item). The Linux version of dcm2niix is compiled on a <span class="p">[</span><span class="nv" style="color: #008080;">holy build box</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/phusion/holy-build-box</span><span class="p">)</span>, so it should run on any Linux distribution.</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"><span class="p"> -</span> If you have a MacOS computer with Homebrew you can run <span class="sb" style="color: #d14;">`brew install dcm2niix`</span>.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,7 +122,7 @@ The following tools exploit dcm2niix</td>
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<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">abcd-dicom2bids</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/DCAN-Labs/abcd-dicom2bids</span><span class="p">)</span> selectively downloads high quality ABCD datasets. </span>
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<td class="old_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">autobids</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/khanlab/autobids</span><span class="p">)</span> automates dcm2bids which uses dcm2niix.</span>
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<td class="old_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">BiDirect_BIDS_Converter</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/wulms/BiDirect_BIDS_Converter</span><span class="p">)</span> for conversion from DICOM to the BIDS standard.</span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">BIDScoin</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/Donders-Institute/bidscoin</span><span class="p">)</span> is a DICOM to BIDS converter with thorough <span class="p">[</span><span class="nv" style="color: #008080;">documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bi<span class="idiff left right">rcibrain.github.io/computingguide/docs/bids/bidscoin</span></span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">BIDScoin</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/Donders-Institute/bidscoin</span><span class="p">)</span> is a DICOM to BIDS converter with <span class="idiff left">a GUI and </span>thorough <span class="p">[</span><span class="nv" style="color: #008080;">documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bi<span class="idiff right">dscoin.readthedocs.io</span></span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">BIDS Toolbox</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/cardiff-brain-research-imaging-centre/bids-toolbox</span><span class="p">)</span> is a web service for the creation and manipulation of BIDS datasets, using dcm2niix for importing DICOM data.</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">birc-bids</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/bircibrain/birc-bids</span><span class="p">)</span> provides a Docker/Singularity container with various BIDS conversion utilities.</span>
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<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">BOLD5000_autoencoder</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/nmningmei/BOLD5000_autoencoder</span><span class="p">)</span> uses dcm2niix to pipe imaging data into an unsupervised machine learning algorithm.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,7 +162,7 @@ The following tools exploit dcm2niix</td>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Neuroinformatics Database (NiDB)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/gbook/nidb</span><span class="p">)</span> is designed to store, retrieve, analyze, and share neuroimaging data. It uses dcm2niix for image QA and handling some formats. </span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">NiftyPET</span><span class="p">](</span><span class="sx" style="color: #d14;">https://niftypet.readthedocs.io/en/latest/install.html</span><span class="p">)</span> provides PET image reconstruction and analysis, and uses dcm2niix to handle DICOM images. </span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">nipype</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/nipy/nipype</span><span class="p">)</span> can use dcm2niix to convert images.</span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;"><span class="idiff left">PNL-nipype</span></span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pnlbwh/<span class="idiff">Dummy-PNL-nipype</span></span><span class="p">)</span> is a Python <span class="idiff right">script</span> that can convert dcm2niix created NIfTI files to the popular NRRD format (including DWI gradient tables). Note, recent versions of dcm2niix can directly convert DICOM images to NRRD.</span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;"><span class="idiff left">conversion</span></span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pnlbwh/<span class="idiff">conversion</span></span><span class="p">)</span> is a Python <span class="idiff right">library</span> that can convert dcm2niix created NIfTI files to the popular NRRD format (including DWI gradient tables). Note, recent versions of dcm2niix can directly convert DICOM images to NRRD.</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">pydcm2niix is a Python module for working with dcm2niix</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/jstutters/pydcm2niix</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">pyBIDSconv provides a graphical format for converting DICOM images to the BIDS format</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/DrMichaelLindner/pyBIDSconv</span><span class="p">)</span>. It includes clever default heuristics for identifying Siemens scans.</span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">qsm</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/CAIsr/qsm</span><span class="p">)</span> Quantitative Susceptibility Mapping software.</span>
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<li id="8695819d77758369f3264b90f25fdd66b2231dde">
<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#8695819d77758369f3264b90f25fdd66b2231dde"><strong>UIH/README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ UIH supports two ways of archiving the DWI/DTI and fMRI data. One way is one DIC</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown">Tag ID | Tag Name | VR | VM | Description | Sample</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown">-- | -- | -- | -- | -- | --</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">0061,1002 | Generate Private | US | 1 | Flag to generate private format file | 1</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**</span>0061,4002<span class="idiff">**</span></span> | <span class="gs" style="font-weight: 600;"><span class="idiff">**</span>FOV<span class="idiff right">**</span></span> | SH | 1 | FOV(mm) | 224<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>224</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">0061,4002 | FOV | SH | 1 | FOV(mm) | 224<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>224</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown">0065,1000 | MeasurmentUID | UL | 1 | Measurement UID of Protocol | 12547865</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown">0065,1002 | ImageOrientationDisplayed | SH | 1 | Image Orientation Displayed | Sag or Sag>Cor</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown">0065,1003 | ReceiveCoil | LO | 1 | Receive Coil Information | H 8</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,9 +21,9 @@ Tag ID | Tag Name | VR | VM | Description | Sample</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">0065,1006 | Slice Group ID | IS | 1 | Slice Group ID | 1</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown">0065,1007 | Uprotocol | OB | 1 | Uprotocol value | </span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown">0065,1009 | BActualValue | FD | 1 | Actual B-Value from sequence | 1000.0</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**</span>0065,100A<span class="idiff">**</span></span> | <span class="gs" style="font-weight: 600;"><span class="idiff">**</span>BUserValue<span class="idiff right">**</span></span> | FD | 1 | User Choose B-Value from UI | 1000.0</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**</span>0065,100B<span class="idiff">**</span></span> | <span class="gs" style="font-weight: 600;"><span class="idiff">**</span>Block Size<span class="idiff right">**</span></span> | DS | 1 | Size of the paradigm/block | 10</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**</span>0065,100C<span class="idiff">**</span></span> | <span class="gs" style="font-weight: 600;"><span class="idiff">**</span>Experimental status<span class="idiff right">**</span></span> | SH | 1 | fMRI | rest/active</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">0065,100A | BUserValue | FD | 1 | User Choose B-Value from UI | 1000.0</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">0065,100B | Block Size | DS | 1 | Size of the paradigm/block | 10</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown">0065,100C | Experimental status | SH | 1 | fMRI | rest/active</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown">0065,100D | Parallel Information | SH | 1 | ratio of parallel acquisition and acceleration | </span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">0065,100F | Slice Position | SH | 1 | Slice location displayed on the screen | H23.4</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown">0065,1011 | Sections | SH | 1 | | </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,17 +38,17 @@ Tag ID | Tag Name | VR | VM | Description | Sample</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown">0065,1029 | AcquisitionDuration | SH | 1 | Acquisition Duration | 0.03</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown">0065,102B | ApplicationCategory | LT | 1 | Application names available | DTI<span class="se" style="color: #d14;">\F</span>unc</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown">0065,102C | RepeatitionIndex | IS | 1 | | 0</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**</span>0065,102D<span class="idiff">**</span></span> | <span class="gs" style="font-weight: 600;"><span class="idiff">**</span>SequenceDisplayName<span class="idiff right">**</span></span> | ST | 1 | Sequence display name | Epi_dti_b0</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown">0065,102D | SequenceDisplayName | ST | 1 | Sequence display name | Epi_dti_b0</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown">0065,102E | NoiseDecovarFlag | LO | 1 | Noise decorrelation flag | PreWhite</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown">0065,102F | ScaleFactor | FL | 1 | scale factor | 2.125</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown">0065,1031 | MRSequenceVariant | SH | 1 | SequenceVariant | </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown">0065,1032 | MRKSpaceFilter | SH | 1 | K space filter | </span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown">0065,1033 | MRTableMode | SH | 1 | Table mode | Fix</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown">0065,1036 | MRDiscoParameter | OB | 1 | | </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**</span>0065,1037<span class="idiff">**</span></span> | <span class="gs" style="font-weight: 600;"><span class="idiff">**</span>MRDiffusionGradOrientation<span class="idiff right">**</span></span> | FD | 3 | Diffusion gradient orientation | 0<span class="se" style="color: #d14;">\0\0</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown">0065,1037 | MRDiffusionGradOrientation | FD | 3 | Diffusion gradient orientation | 0<span class="se" style="color: #d14;">\0\0</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown">0065,1038 | MRPerfusionNoiseLevel | FD | 1 | epi_dwi/perfusion noise level | 40</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown">0065,1039 | MRGradRange | SH | 6 | linear range of gradient | 0.0<span class="se" style="color: #d14;">\1</span>57<span class="se" style="color: #d14;">\0</span>.0<span class="se" style="color: #d14;">\1</span>57<span class="se" style="color: #d14;">\0</span>.0<span class="se" style="color: #d14;">\1</span>25</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**</span>0065,1050<span class="idiff">**</span></span> | <span class="gs" style="font-weight: 600;"><span class="idiff">**</span>MR Number Of Slice In Volume<span class="idiff right">**</span></span> | DS | 1 | Number Of Frames In a Volume，Columns of each frame: cols =ceil(sqrt(total)) ; Rows of each frame: rows =ceil(total/cols) ; appeared when image type (00080008) has VFRAME | 27</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown">0065,1050 | MR Number Of Slice In Volume | DS | 1 | Number Of Frames In a Volume，Columns of each frame: cols =ceil(sqrt(total)) ; Rows of each frame: rows =ceil(total/cols) ; appeared when image type (00080008) has VFRAME | 27</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown">0065,1051 | MR VFrame Sequence | SQ | 1 | 1 | </span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"> ->0008,0022 | Acquisition Date | DA | 1 | | </span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"> ->0008,0032 | Acquisition Time | TM | 1 | | </span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#d19bcb068e96ecf84a2a5f6708a2d78f166177ff"><strong>console/CMakeLists.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,10 +53,15 @@ endif()</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Compiler dependent flags</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span> <span class="p">(</span>CheckCXXCompilerFlag<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>UNIX<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">check_cxx_compiler_flag</span><span class="p">(</span>-msse2 HAS_SSE2<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>HAS_SSE2<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -msse2 -mfpmath=sse"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">check_cxx_compiler_flag</span><span class="p">(</span>-march=armv8-a+crc ARM_CRC<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>ARM_CRC<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># wrong answer for Apple Silicon: check_cxx_compiler_flag(-msse2 HAS_SSE2)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">check_cxx_compiler_flag</span><span class="p">(</span>-msse2 HAS_SSE2<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>HAS_SSE2<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -msse2 -mfpmath=sse"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PROGRAMS dcm2niix<span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#6161009529e5e4e6364b2f49e592dc6ea75e4594"><strong>console/main_console.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,7 +88,7 @@ void showHelp(const char * argv[], struct TDCMopts opts) {</td>
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88
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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89
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define kQstr ""</span></span>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -f : filename (%%a=antenna (coil) name, %%b=basename, %%c=comments, %%d=description, %%e=echo number, %%f=folder name, %%i=ID of patient, %%j=seriesInstanceUID, %%k=studyInstanceUID, %%m=manufacturer, %%n=name of patient, %%o=mediaObjectInstanceUID, %%p=protocol,%s %%r=instance number, %%s=series number, %%t=time, %%u=acquisition number, %%v=vendor, %%x=study ID; %%z=sequence name; default '%s')</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">kQstr</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -f : filename (%%a=antenna (coil) name, %%b=basename, %%c=comments, %%d=description, %%e=echo number, %%f=folder name, <span class="idiff left right">%%g=accession number, </span>%%i=ID of patient, %%j=seriesInstanceUID, %%k=studyInstanceUID, %%m=manufacturer, %%n=name of patient, %%o=mediaObjectInstanceUID, %%p=protocol,%s %%r=instance number, %%s=series number, %%t=time, %%u=acquisition number, %%v=vendor, %%x=study ID; %%z=sequence name; default '%s')</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">kQstr</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -g : generate defaults file (y/n/o/i [o=only: reset and write defaults; i=ignore: reset defaults], default n)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -h : show help</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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94
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -i : ignore derived, localizer and 2D images (y/n, default n)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +102,8 @@ void showHelp(const char * argv[], struct TDCMopts opts) {</td>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -p : Philips precise float (not display) scaling (y/n, default y)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -r : rename instead of convert DICOMs (y/n, default n)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -s : single file mode, do not convert other images in folder (y/n, default n)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -t : text notes includes private patient details (y/n, default n)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//text notes replaced with BIDS: this function is deprecated</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf(" -t : text notes includes private patient details (y/n, default n)\n");</span></span>
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106
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if !defined(_WIN64) && !defined(_WIN32) //shell script for Unix only</span></span>
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107
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -u : up-to-date check</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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108
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -399,9 +400,14 @@ int main(int argc, const char * argv[])</td>
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399
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isForceStackSameSeries</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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400
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'2'</span><span class="p">))</span></span>
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401
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isForceStackSameSeries</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'O'</span><span class="p">))</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'O'</span><span class="p">))</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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403
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isForceStackDCE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="cpp"></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("Advanced feature: '-m o' merges images despite varying series number\n");</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="p">}</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'2'</span><span class="p">))</span> <span class="p">{</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isIgnoreSeriesInstanceUID</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Advanced feature: '-m 2' ignores Series Instance UID.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">invalidParam</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<li id="5960b99778897bf78ce0e20de3260a5c26016eec">
<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#5960b99778897bf78ce0e20de3260a5c26016eec"><strong>console/nifti1_io_core.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -192,6 +192,18 @@ vec3 nifti_vect33_norm (vec3 v) { //normalize vector length</td>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vO</span><span class="p">;</span></span>
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193
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"><span class="p">}</span></span>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"><span class="n" style="color: #333;">vec4</span> <span class="nf" style="color: #900; font-weight: 600;">nifti_vect44_norm</span> <span class="p">(</span><span class="n" style="color: #333;">vec4</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//normalize vector length</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="n" style="color: #333;">vec4</span> <span class="n" style="color: #333;">vO</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">vLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]));</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vLen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">FLT_EPSILON</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vO</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//avoid divide by zero</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">vO</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">vLen</span><span class="p">;</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vO</span><span class="p">;</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"><span class="n" style="color: #333;">vec3</span> <span class="nf" style="color: #900; font-weight: 600;">nifti_vect33mat33_mul</span><span class="p">(</span><span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">mat33</span> <span class="n" style="color: #333;">m</span> <span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//multiply vector * 3x3matrix</span></span>
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196
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">vO</span><span class="p">;</span></span>
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197
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//multiply Pcrs * m</span></span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#966be9a60ccbbd15be352c99c24de65122ff7e63"><strong>console/nifti1_io_core.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,6 +68,7 @@ mat44 nifti_mat44_inverse( mat44 R );</td>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"><span class="n" style="color: #333;">mat44</span> <span class="n" style="color: #333;">nifti_mat44_mul</span><span class="p">(</span> <span class="n" style="color: #333;">mat44</span> <span class="n" style="color: #333;">A</span> <span class="p">,</span> <span class="n" style="color: #333;">mat44</span> <span class="n" style="color: #333;">B</span> <span class="p">);</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">crossProduct</span><span class="p">(</span><span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">u</span><span class="p">,</span> <span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"><span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">nifti_vect33_norm</span> <span class="p">(</span><span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"><span class="n" style="color: #333;">vec4</span> <span class="n" style="color: #333;">nifti_vect44_norm</span> <span class="p">(</span><span class="n" style="color: #333;">vec4</span> <span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"><span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">nifti_vect33mat33_mul</span><span class="p">(</span><span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">mat33</span> <span class="n" style="color: #333;">m</span> <span class="p">);</span></span>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="n" style="color: #333;">ivec3</span> <span class="n" style="color: #333;">setiVec3</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"><span class="n" style="color: #333;">vec3</span> <span class="n" style="color: #333;">setVec3</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#7f920a885f04d331121e6efbfd08cb9080cb5038"><strong>console/nii_dicom.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -739,6 +739,11 @@ struct TDICOMdata clear_dicom_data() {</td>
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739
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739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">coilName</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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740
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">coilElements</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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741
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">radiopharmaceutical</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">convolutionKernel</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">unitsPT</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">decayCorrection</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">attenuationCorrectionMethod</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">reconstructionMethod</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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742
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747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">phaseEncodingLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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743
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//~ d.patientPositionSequentialRepeats = 0;</span></span>
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744
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749
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//~ d.patientPositionRepeats = 0;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -805,6 +810,7 @@ struct TDICOMdata clear_dicom_data() {</td>
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805
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">is2DAcq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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806
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//0008,0008 = DERIVED,CSAPARALLEL,POSDISP</span></span>
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807
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isSegamiOasis</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//these images do not store spatial coordinates</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isBVecWorldCoordinates</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//bvecs can be in image space (GE) or world coordinates (Siemens)</span></span>
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808
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isGrayscaleSoftcopyPresentationState</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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809
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isRawDataStorage</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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810
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isPartialFourier</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -848,6 +854,7 @@ struct TDICOMdata clear_dicom_data() {</td>
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848
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854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">overlayStart</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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849
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasOverlay</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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850
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isPrivateCreatorRemap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isRealIsPhaseMapHz</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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851
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">numberOfImagesInGridUIH</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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852
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">phaseEncodingRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">;</span></span>
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853
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860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">patientSex</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1133,9 +1140,8 @@ int dcmStrManufacturer (const int lByteLength, unsigned char lBuffer[]) {//read</td>
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1133
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// char cString[lByteLength + 1];</span></span>
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1134
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<td class="new_line diff-line-num" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#endif</span></span>
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1135
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMANUFACTURER_UNKNOWN</span><span class="p">;</span></span>
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1136
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<pre style="margin: 0;">-<span id="LC1136" class="line" lang="cpp"> <span class="n" style="color: #333;">cString</span><span class="p">[</span><span class="n" style="color: #333;">lByteLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="cpp"> <span class="n" style="color: #333;">cString</span><span class="p">[</span><span class="n" style="color: #333;">lByteLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="idiff left right"> </span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1137
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">cString</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lBuffer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">lByteLength</span><span class="p">);</span></span>
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1138
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<pre style="margin: 0;">-<span id="LC1138" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("MANU %s\n",cString);</span></span>
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1139
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1145
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">cString</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'S'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">cString</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">))</span></span>
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1140
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1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMANUFACTURER_SIEMENS</span><span class="p">;</span></span>
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1141
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">cString</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">cString</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'E'</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1153,6 +1159,8 @@ int dcmStrManufacturer (const int lByteLength, unsigned char lBuffer[]) {//read</td>
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1153
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1159
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<pre style="margin: 0;"> <span id="LC1159" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMANUFACTURER_UIH</span><span class="p">;</span></span>
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1154
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1160
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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">cString</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'B'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">cString</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1155
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<td class="new_line diff-line-num" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1161
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMANUFACTURER_BRUKER</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_UNKNOWN</span><span class="p">)</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown manufacturer %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">cString</span><span class="p">);</span></span>
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1156
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1164
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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#ifdef _MSC_VER</span></span>
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1157
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">cString</span><span class="p">);</span></span>
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1158
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1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1237,7 +1245,8 @@ void checkSliceTimes(struct TCSAdata *CSA, int itemsOK, int isVerbose, bool is3D</td>
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1237
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Nov 1, 2018 <siemens-healthineers.com> wrote:</span></span>
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1238
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1246
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If you have an interleaved dataset we can more definitively validate this formula (aka sliceTime(i) - min(sliceTimes())).</span></span>
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1239
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1247
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">minTimeValue</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1240
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<pre style="margin: 0;">-<span id="LC1240" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Adjusting for negative MosaicRefAcqTimes (issue 271).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printWarning("Adjusting for negative MosaicRefAcqTimes (issue 271).\n"); //if uncommented, overwhelming number of warnings (one per DICOM input), better once per series</span></span>
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1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="cpp"> <span class="n" style="color: #333;">CSA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="n" style="color: #333;">kMaxEPI3D</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">2.0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//issue 271: flag for unified warning</span></span>
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1241
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1250
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">itemsOK</span><span class="p">;</span> <span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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1242
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1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="cpp"> <span class="n" style="color: #333;">CSA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CSA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">minTimeValue</span><span class="p">;</span></span>
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1243
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1252
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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1646,15 +1655,13 @@ int isSameFloatGE (float a, float b) {</td>
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1646
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1655
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<pre style="margin: 0;"> <span id="LC1655" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">0.0001</span><span class="p">);</span></span>
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1647
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1656
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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="cpp"><span class="p">}</span></span>
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1648
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1657
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<pre style="margin: 0;"> <span id="LC1657" class="line" lang="cpp"></span>
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1649
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<pre style="margin: 0;">-<span id="LC1649" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="nf" style="color: #900; font-weight: 600;">nii_readParRec</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">parname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dti4D</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isReadPhase</span><span class="p">)</span> <span class="p">{</span></span>
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1658
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<pre style="margin: 0;">+<span id="LC1658" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="nf" style="color: #900; font-weight: 600;">nii_readParRec</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">parname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dti4D</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isReadPhase</span><span class="p">)</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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1650
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1659
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<pre style="margin: 0;"> <span id="LC1659" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clear_dicom_data</span><span class="p">();</span></span>
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1651
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1660
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sliceOrder</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1652
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1661
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<pre style="margin: 0;"> <span id="LC1661" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">volumeOnsetTime</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1653
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1662
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<pre style="margin: 0;"> <span id="LC1662" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">decayFactor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1654
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1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">frameDuration</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1655
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1664
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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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1656
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<pre style="margin: 0;">-<span id="LC1656" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">repetitionTimeExcitation</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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1657
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<pre style="margin: 0;">-<span id="LC1657" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">repetitionTimeInversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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1658
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1665
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="cpp"><span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//erase dummy with empty</span></span>
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1659
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<td class="new_line diff-line-num" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1666
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="cpp"><span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesDescription</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//erase dummy with empty</span></span>
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1660
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<td class="new_line diff-line-num" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1667
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<pre style="margin: 0;"> <span id="LC1667" class="line" lang="cpp"><span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//erase dummy with empty</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1769,7 +1776,7 @@ int kbval = 33; //V3: 27</td>
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1769
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1776
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<pre style="margin: 0;"> <span id="LC1776" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxNumberOfCardiacPhases</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxNumberOfEchoes</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxNumberOfDynamics</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxNumberOfMixes</span><span class="p">;</span></span>
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1770
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1777
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<pre style="margin: 0;"> <span id="LC1777" class="line" lang="cpp"> <span class="n" style="color: #333;">num2DExpected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">num3DExpected</span><span class="p">;</span></span>
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1771
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1778
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<pre style="margin: 0;"> <span id="LC1778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">num2DExpected</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">kMaxSlice2D</span><span class="p">)</span> <span class="p">{</span></span>
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1772
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<pre style="margin: 0;">-<span id="LC1772" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Use dicm2nii or increase kMax<span class="idiff left right">DTI4</span>D to be more than %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">num2DExpected</span><span class="p">);</span></span>
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1779
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<pre style="margin: 0;">+<span id="LC1779" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Use dicm2nii or increase kMax<span class="idiff left right">Slice2</span>D to be more than %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">num2DExpected</span><span class="p">);</span></span>
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1773
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1780
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<pre style="margin: 0;"> <span id="LC1780" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" slices*grad*bval*cardiac*echo*dynamic*mix*label = %d*%d*%d*%d*%d*%d*%d*%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1774
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1781
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">maxNumberOfGradientOrients</span><span class="p">,</span><span class="n" style="color: #333;">maxNumberOfDiffusionValues</span><span class="p">,</span></span>
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1775
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1782
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<pre style="margin: 0;"> <span id="LC1782" class="line" lang="cpp"> <span class="n" style="color: #333;">maxNumberOfCardiacPhases</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfEchoes</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfDynamics</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfMixes</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfLabels</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1970,11 +1977,10 @@ int kbval = 33; //V3: 27</td>
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1970
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1977
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<pre style="margin: 0;"> <span id="LC1977" class="line" lang="cpp"> <span class="p">}</span></span>
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1971
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1978
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<pre style="margin: 0;"> <span id="LC1978" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//diskSlice ++;</span></span>
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1972
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1979
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<pre style="margin: 0;"> <span id="LC1979" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isADC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1973
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<td class="new_line diff-line-num old" data-linenumber="1980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1973" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">maxNumberOfGradientOrients</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kbval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">50</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isSameFloat</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kv1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isSameFloat</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kv2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isSameFloat</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kv<span class="idiff left right">2</span></span><span class="p">])</span> <span class="p">)</span> <span class="p">{</span></span>
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1980
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<pre style="margin: 0;">+<span id="LC1980" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">maxNumberOfGradientOrients</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kbval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">50</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isSameFloat</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kv1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isSameFloat</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kv2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isSameFloat</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kv<span class="idiff left right">3</span></span><span class="p">])</span> <span class="p">)</span> <span class="p">{</span></span>
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1974
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1981
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<pre style="margin: 0;"> <span id="LC1981" class="line" lang="cpp"> <span class="n" style="color: #333;">isADC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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1975
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1982
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<pre style="margin: 0;"> <span id="LC1982" class="line" lang="cpp"> <span class="n" style="color: #333;">ADCwarning</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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1976
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1983
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<pre style="margin: 0;"> <span id="LC1983" class="line" lang="cpp"> <span class="p">}</span></span>
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1977
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<td class="new_line diff-line-num old" data-linenumber="1984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1977" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage(">>%d %d\n", (int)cols[kSlice], diskSlice);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1978
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1984
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<pre style="margin: 0;"> <span id="LC1984" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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1979
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1985
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<pre style="margin: 0;"> <span id="LC1985" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzMM</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kXmm</span><span class="p">];</span></span>
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1980
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<td class="new_line diff-line-num" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1986
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<pre style="margin: 0;"> <span id="LC1986" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzMM</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kYmm</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2019,9 +2025,10 @@ int kbval = 33; //V3: 27</td>
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2019
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2025
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<pre style="margin: 0;"> <span id="LC2025" class="line" lang="cpp"> <span class="p">}</span></span>
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2020
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2026
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<pre style="margin: 0;"> <span id="LC2026" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasMagnitude</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2021
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<td class="new_line diff-line-num" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2027
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<pre style="margin: 0;"> <span id="LC2027" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasPhase</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2022
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<td class="new_line diff-line-num old" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2022" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isSameFloat</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">],</span><span class="mi" style="color: #099;">18</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isTypeWarning</span><span class="p">))</span> <span class="p">{</span></span>
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2023
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<td class="new_line diff-line-num old" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2023" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Field map in Hz will be saved as the 'real' image.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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2024
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<td class="new_line diff-line-num old" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2024" class="line" lang="cpp"> <span class="n" style="color: #333;">isTypeWarning</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2028
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<pre style="margin: 0;">+<span id="LC2028" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSameFloat</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">],</span><span class="mi" style="color: #099;">18</span><span class="p">))</span> <span class="p">{</span></span>
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2029
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<pre style="margin: 0;">+<span id="LC2029" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printWarning("Field map in Hz will be saved as the 'real' image.\n");</span></span>
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2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//isTypeWarning = true;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2031
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<pre style="margin: 0;">+<span id="LC2031" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isRealIsPhaseMapHz</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2025
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<td class="new_line diff-line-num" data-linenumber="2032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2032
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<pre style="margin: 0;"> <span id="LC2032" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">4.0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isTypeWarning</span><span class="p">))</span> <span class="p">{</span></span>
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2026
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<td class="new_line diff-line-num" data-linenumber="2033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2033
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown type %g: not magnitude[0], real[1], imaginary[2] or phase[3].</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]);</span></span>
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2027
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2034
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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="cpp"> <span class="n" style="color: #333;">isTypeWarning</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2109,6 +2116,10 @@ int kbval = 33; //V3: 27</td>
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2109
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2116
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<pre style="margin: 0;"> <span id="LC2116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isReal</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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2110
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2117
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<pre style="margin: 0;"> <span id="LC2117" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isImaginary</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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2111
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2118
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<pre style="margin: 0;"> <span id="LC2118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isPhase</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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2119
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<pre style="margin: 0;">+<span id="LC2119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">18</span><span class="p">)</span> <span class="p">{</span></span>
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2120
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<pre style="margin: 0;">+<span id="LC2120" class="line" lang="cpp"> <span class="n" style="color: #333;">isReal</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2121
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<pre style="margin: 0;">+<span id="LC2121" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isRealIsPhaseMapHz</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2122
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<pre style="margin: 0;">+<span id="LC2122" class="line" lang="cpp"> <span class="p">}</span> </span>
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2112
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2123
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<pre style="margin: 0;"> <span id="LC2123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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2113
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2124
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<pre style="margin: 0;"> <span id="LC2124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isType4Warning</span><span class="p">)</span> <span class="p">{</span></span>
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2114
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2125
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<pre style="margin: 0;"> <span id="LC2125" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown image type (4). Be aware the 'phase' image is of an unknown type.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2116,8 +2127,13 @@ int kbval = 33; //V3: 27</td>
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2116
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2127
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<pre style="margin: 0;"> <span id="LC2127" class="line" lang="cpp"> <span class="p">}</span></span>
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2117
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2128
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<pre style="margin: 0;"> <span id="LC2128" class="line" lang="cpp"> <span class="n" style="color: #333;">isPhase</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//2019</span></span>
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2118
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2129
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<pre style="margin: 0;"> <span id="LC2129" class="line" lang="cpp"> <span class="p">}</span></span>
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2119
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<pre style="margin: 0;">-<span id="LC2119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">3.0</span><span class="p">))</span></span>
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2130
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<pre style="margin: 0;">+<span id="LC2130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">18</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">3.0</span><span class="p">)))</span> <span class="p">{</span></span>
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2131
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<pre style="margin: 0;">+<span id="LC2131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isType4Warning</span><span class="p">)</span> <span class="p">{</span></span>
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2132
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<pre style="margin: 0;">+<span id="LC2132" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown image type (%g). Be aware the 'phase' image is of an unknown type.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">round</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kImageType</span><span class="p">]));</span></span>
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2133
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<pre style="margin: 0;">+<span id="LC2133" class="line" lang="cpp"> <span class="n" style="color: #333;">isType4Warning</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2134
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<pre style="margin: 0;">+<span id="LC2134" class="line" lang="cpp"> <span class="p">}</span></span>
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2120
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2135
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<pre style="margin: 0;"> <span id="LC2135" class="line" lang="cpp"> <span class="n" style="color: #333;">isReal</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//<- this is not correct, kludge for bug in ROGERS_20180526_WIP_B0_NS_8_1.PAR</span></span>
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2136
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<pre style="margin: 0;">+<span id="LC2136" class="line" lang="cpp"> <span class="p">}</span></span>
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2121
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2137
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<pre style="margin: 0;"> <span id="LC2137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isReal</span><span class="p">)</span> <span class="n" style="color: #333;">vol</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">num3DExpected</span><span class="p">;</span></span>
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2122
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2138
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<pre style="margin: 0;"> <span id="LC2138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isImaginary</span><span class="p">)</span> <span class="n" style="color: #333;">vol</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num3DExpected</span><span class="p">);</span></span>
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2123
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2139
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<pre style="margin: 0;"> <span id="LC2139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isPhase</span><span class="p">)</span> <span class="n" style="color: #333;">vol</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num3DExpected</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2129,7 +2145,7 @@ int kbval = 33; //V3: 27</td>
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2129
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2145
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<pre style="margin: 0;"> <span id="LC2145" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span> <span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">);</span></span>
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2130
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2146
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<pre style="margin: 0;"> <span id="LC2146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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2131
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2147
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<pre style="margin: 0;"> <span id="LC2147" class="line" lang="cpp"> <span class="p">}</span></span>
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2132
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<pre style="margin: 0;">-<span id="LC2132" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;">// dti4D->S[vol].V[0] = cols[kbval];</span></span>
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2148
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<pre style="margin: 0;">+<span id="LC2148" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// dti4D->S[vol].V[0] = cols[kbval];</span></span>
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2133
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2149
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<pre style="margin: 0;"> <span id="LC2149" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//dti4D->gradDynVol[vol] = gradDynVol;</span></span>
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2134
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2150
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<pre style="margin: 0;"> <span id="LC2150" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">TE</span><span class="p">[</span><span class="n" style="color: #333;">vol</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kTEcho</span><span class="p">];</span></span>
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2135
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2151
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<pre style="margin: 0;"> <span id="LC2151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kTEcho</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2152,7 +2168,7 @@ int kbval = 33; //V3: 27</td>
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2152
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2168
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<pre style="margin: 0;"> <span id="LC2168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">vol</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span><span class="p">)</span></span>
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2153
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2169
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<pre style="margin: 0;"> <span id="LC2169" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vol</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2154
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2170
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<pre style="margin: 0;"> <span id="LC2170" class="line" lang="cpp"> <span class="p">}</span></span>
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2155
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<pre style="margin: 0;">-<span id="LC2155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kMax<span class="idiff left right">Slice2</span>D</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//issue 363: intensity can vary with each 2D slice of 4D volume</span></span>
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2171
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<pre style="margin: 0;">+<span id="LC2171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kMax<span class="idiff left right">DTI4</span>D</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//issue 363: intensity can vary with each 2D slice of 4D volume</span></span>
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2156
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2172
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<pre style="margin: 0;"> <span id="LC2172" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("%d %g %g\n", numSlice2D, cols[kRI], cols[kRS]);</span></span>
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2157
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2173
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<pre style="margin: 0;"> <span id="LC2173" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenIntercept</span><span class="p">[</span><span class="n" style="color: #333;">numSlice2D</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kRI</span><span class="p">];</span></span>
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2158
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2174
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<pre style="margin: 0;"> <span id="LC2174" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="n" style="color: #333;">numSlice2D</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">kRS</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2179,6 +2195,14 @@ int kbval = 33; //V3: 27</td>
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2179
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2195
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<pre style="margin: 0;"> <span id="LC2195" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Invalid PAR format header (unable to detect version or slices) %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">parname</span><span class="p">);</span></span>
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2180
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2196
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<pre style="margin: 0;"> <span id="LC2196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2181
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2197
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<pre style="margin: 0;"> <span id="LC2197" class="line" lang="cpp"> <span class="p">}</span></span>
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2198
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<pre style="margin: 0;">+<span id="LC2198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kMaxSlice2D</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//check again after reading, as top portion of header does not report image types or isotropics</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2199
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<pre style="margin: 0;">+<span id="LC2199" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Increase kMaxSlice2D from %d to at least %d (or use dicm2nii).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxSlice2D</span><span class="p">,</span> <span class="n" style="color: #333;">numSlice2D</span><span class="p">);</span></span>
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2200
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<pre style="margin: 0;">+<span id="LC2200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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2201
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<pre style="margin: 0;">+<span id="LC2201" class="line" lang="cpp"> <span class="p">}</span></span>
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2202
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<pre style="margin: 0;">+<span id="LC2202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kMaxDTI4D</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//since issue460, kMaxSlice2D == kMaxSlice4D, so we should never get here</span></span>
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2203
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<pre style="margin: 0;">+<span id="LC2203" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Increase kMaxDTI4D from %d to at least %d (or use dicm2nii).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxDTI4D</span><span class="p">,</span> <span class="n" style="color: #333;">numSlice2D</span><span class="p">);</span></span>
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2204
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<pre style="margin: 0;">+<span id="LC2204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</span><span class="p">;</span> </span>
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2205
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<pre style="margin: 0;">+<span id="LC2205" class="line" lang="cpp"> <span class="p">}</span></span>
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2182
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2206
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<pre style="margin: 0;"> <span id="LC2206" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMANUFACTURER_PHILIPS</span><span class="p">;</span></span>
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2183
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2207
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<pre style="margin: 0;"> <span id="LC2207" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isValid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2184
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2208
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<pre style="margin: 0;"> <span id="LC2208" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isSigned</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2203,10 +2227,6 @@ int kbval = 33; //V3: 27</td>
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2203
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2227
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<pre style="margin: 0;"> <span id="LC2227" class="line" lang="cpp"> <span class="p">}</span></span>
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2204
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2228
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<pre style="margin: 0;"> <span id="LC2228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxVol</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//e.g. gradient 2 can skip B=0 but include isotropic</span></span>
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2205
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2229
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<pre style="margin: 0;"> <span id="LC2229" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//remove unused slices - this will happen if unless we have all 4 image types: real, imag, mag, phase</span></span>
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2206
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<pre style="margin: 0;">-<span id="LC2206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kMaxSlice2D</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//check again after reading, as top portion of header does not report image types or isotropics</span></span>
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2207
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<pre style="margin: 0;">-<span id="LC2207" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Increase kMaxSlice2D from %d to at least %d (or use dicm2nii).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxSlice2D</span><span class="p">,</span> <span class="n" style="color: #333;">numSlice2D</span><span class="p">);</span></span>
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2208
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<td class="new_line diff-line-num old" data-linenumber="2230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2208" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isValid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2209
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<td class="new_line diff-line-num old" data-linenumber="2230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2209" class="line" lang="cpp"> <span class="p">}</span></span>
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2210
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2230
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<pre style="margin: 0;"> <span id="LC2230" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2211
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<td class="new_line diff-line-num" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2231
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<pre style="margin: 0;"> <span id="LC2231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kMaxSlice2D</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2212
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<td class="new_line diff-line-num" data-linenumber="2232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2232
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<pre style="margin: 0;"> <span id="LC2232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sliceOrder</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//this slice was populated</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2242,7 +2262,7 @@ int kbval = 33; //V3: 27</td>
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2242
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2262
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<pre style="margin: 0;"> <span id="LC2262" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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2243
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2263
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<pre style="margin: 0;"> <span id="LC2263" class="line" lang="cpp"> <span class="p">}</span></span>
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2244
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2264
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<pre style="margin: 0;"> <span id="LC2264" class="line" lang="cpp"> <span class="p">}</span></span>
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2245
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<pre style="margin: 0;">-<span id="LC2245" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isScaleOrTEVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2265
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<pre style="margin: 0;">+<span id="LC2265" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isScaleOrTEVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2246
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2266
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<pre style="margin: 0;"> <span id="LC2266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kMaxSlice2D</span><span class="p">)</span> <span class="p">{</span></span>
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2247
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2267
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<pre style="margin: 0;"> <span id="LC2267" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Overloaded slice re-ordering. Number of slices (%d) exceeds kMaxSlice2D (%d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">numSlice2D</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxSlice2D</span><span class="p">);</span></span>
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2248
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2268
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<pre style="margin: 0;"> <span id="LC2268" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sliceOrder</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2269,14 +2289,14 @@ int kbval = 33; //V3: 27</td>
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2269
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2289
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<pre style="margin: 0;"> <span id="LC2289" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Reported TR=%gms, measured TR=%gms (prospect. motion corr.?)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">TR</span><span class="p">,</span> <span class="n" style="color: #333;">TRms</span><span class="p">);</span></span>
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2270
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2290
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<pre style="margin: 0;"> <span id="LC2290" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">TR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TRms</span><span class="p">;</span></span>
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2271
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2291
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<pre style="margin: 0;"> <span id="LC2291" class="line" lang="cpp"> <span class="p">}</span></span>
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2272
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<pre style="margin: 0;">-<span id="LC2272" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isTypeWarning</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num2DExpected</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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2292
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isTypeWarning</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num2DExpected</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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2273
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<td class="new_line diff-line-num" data-linenumber="2293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2293
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<pre style="margin: 0;"> <span id="LC2293" class="line" lang="cpp"> <span class="n" style="color: #333;">num2DExpected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numSlice2D</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2274
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<td class="new_line diff-line-num" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2294
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<pre style="margin: 0;"> <span id="LC2294" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2275
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<td class="new_line diff-line-num" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2295
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<pre style="margin: 0;"> <span id="LC2295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">((</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num2DExpected</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2276
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<td class="new_line diff-line-num" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2296
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<pre style="margin: 0;"> <span id="LC2296" class="line" lang="cpp"> <span class="n" style="color: #333;">num2DExpected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2277
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<td class="new_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2297
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<pre style="margin: 0;"> <span id="LC2297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ADCwarning</span><span class="p">)</span> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"More volumes than described in header (ADC or isotropic?)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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2278
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<td class="new_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2298
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<pre style="margin: 0;"> <span id="LC2298" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2279
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<td class="new_line diff-line-num old" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2279" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num2DExpected</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2299
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<pre style="margin: 0;">+<span id="LC2299" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">numSlice2D</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num2DExpected</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2280
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<td class="new_line diff-line-num" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2300
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<pre style="margin: 0;"> <span id="LC2300" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Found %d slices, but expected divisible by %d: slices*grad*bval*cardiac*echo*dynamic*mix*labels = %d*%d*%d*%d*%d*%d*%d*%d %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">numSlice2D</span><span class="p">,</span> <span class="n" style="color: #333;">num2DExpected</span><span class="p">,</span></span>
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2281
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<td class="new_line diff-line-num" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2301
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<pre style="margin: 0;"> <span id="LC2301" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">maxNumberOfGradientOrients</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfDiffusionValues</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2282
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<td class="new_line diff-line-num" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2302
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<pre style="margin: 0;"> <span id="LC2302" class="line" lang="cpp"> <span class="n" style="color: #333;">maxNumberOfCardiacPhases</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfEchoes</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfDynamics</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfMixes</span><span class="p">,</span><span class="n" style="color: #333;">maxNumberOfLabels</span><span class="p">,</span> <span class="n" style="color: #333;">parname</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2438,6 +2458,7 @@ int kbval = 33; //V3: 27</td>
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2438
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<td class="new_line diff-line-num" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2458
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<pre style="margin: 0;"> <span id="LC2458" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2439
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<td class="new_line diff-line-num" data-linenumber="2459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2459
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<pre style="margin: 0;"> <span id="LC2459" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">kMaxDTI4D</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2440
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<td class="new_line diff-line-num" data-linenumber="2460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2460
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<pre style="margin: 0;"> <span id="LC2460" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to convert DTI [increase kMaxDTI4D] found %d directions</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span><span class="p">);</span></span>
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2461
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<pre style="margin: 0;">+<span id="LC2461" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" slices*grad*bval*cardiac*echo*dynamic*mix*label = %d*%d*%d*%d*%d*%d*%d*%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">maxNumberOfGradientOrients</span><span class="p">,</span><span class="n" style="color: #333;">maxNumberOfDiffusionValues</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfCardiacPhases</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfEchoes</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfDynamics</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfMixes</span><span class="p">,</span> <span class="n" style="color: #333;">maxNumberOfLabels</span><span class="p">);</span></span>
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2462
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<pre style="margin: 0;"> <span id="LC2462" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2442
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2463
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<pre style="margin: 0;"> <span id="LC2463" class="line" lang="cpp"> <span class="p">};</span></span>
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2443
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2464
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<pre style="margin: 0;"> <span id="LC2464" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//check if dimensions vary</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4033,12 +4054,22 @@ bool compareTDCMdim (const TDCMdim &dcm1, const TDCMdim &dcm2) {</td>
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4033
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4054
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<pre style="margin: 0;"> <span id="LC4054" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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4034
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4055
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<pre style="margin: 0;"> <span id="LC4055" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//compareTDCMdim()</span></span>
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4035
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4056
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<pre style="margin: 0;"> <span id="LC4056" class="line" lang="cpp"></span>
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4057
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<pre style="margin: 0;">+<span id="LC4057" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">compareTDCMdimRev</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TDCMdim</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dcm1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TDCMdim</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dcm2</span><span class="p">)</span> <span class="p">{</span></span>
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4058
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<pre style="margin: 0;">+<span id="LC4058" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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4059
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<pre style="margin: 0;">+<span id="LC4059" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">dcm1</span><span class="p">.</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dcm2</span><span class="p">.</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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4060
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<pre style="margin: 0;">+<span id="LC4060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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4061
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<pre style="margin: 0;">+<span id="LC4061" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">dcm1</span><span class="p">.</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dcm2</span><span class="p">.</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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4062
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<pre style="margin: 0;">+<span id="LC4062" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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4063
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<pre style="margin: 0;">+<span id="LC4063" class="line" lang="cpp"> <span class="p">}</span></span>
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4064
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<pre style="margin: 0;">+<span id="LC4064" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4065" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//compareTDCMdimRev()</span></span>
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4066
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<pre style="margin: 0;">+<span id="LC4066" class="line" lang="cpp"></span>
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4036
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4067
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<pre style="margin: 0;"> <span id="LC4067" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4037
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4068
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<pre style="margin: 0;"> <span id="LC4068" class="line" lang="cpp"></span>
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4038
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4069
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<pre style="margin: 0;"> <span id="LC4069" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compareTDCMdim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">item1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">item2</span><span class="p">)</span> <span class="p">{</span></span>
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4039
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4070
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<pre style="margin: 0;"> <span id="LC4070" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dcm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">item1</span><span class="p">;</span></span>
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4040
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4071
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<pre style="margin: 0;"> <span id="LC4071" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dcm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">item2</span><span class="p">;</span></span>
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4041
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<pre style="margin: 0;">-<span id="LC4041" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(int i<span class="idiff left">=</span>0; i < MAX_NUMBER_OF_DIMENSIONS; ++<span class="idiff right">i</span>){</span></span>
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4072
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<pre style="margin: 0;">+<span id="LC4072" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for<span class="idiff left"> </span>(int i<span class="idiff"> = </span>0; i < MAX_NUMBER_OF_DIMENSIONS; <span class="idiff">i</span>++)<span class="idiff right"> </span>{</span></span>
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4042
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4073
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<pre style="margin: 0;"> <span id="LC4073" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">){</span></span>
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4043
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4074
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<pre style="margin: 0;"> <span id="LC4074" class="line" lang="cpp"></span>
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4044
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4075
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<pre style="margin: 0;"> <span id="LC4075" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">dcm1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dcm2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4049,6 +4080,18 @@ int compareTDCMdim(void const *item1, void const *item2) {</td>
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4049
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4080
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<pre style="margin: 0;"> <span id="LC4080" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4050
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4081
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<pre style="margin: 0;"> <span id="LC4081" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//compareTDCMdim()</span></span>
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4051
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4082
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<pre style="margin: 0;"> <span id="LC4082" class="line" lang="cpp"></span>
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4083
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<pre style="margin: 0;">+<span id="LC4083" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compareTDCMdimRev</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">item1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">item2</span><span class="p">)</span> <span class="p">{</span></span>
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4084
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<pre style="margin: 0;">+<span id="LC4084" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dcm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">item1</span><span class="p">;</span></span>
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4085
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<pre style="margin: 0;">+<span id="LC4085" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dcm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">item2</span><span class="p">;</span></span>
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4086
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<pre style="margin: 0;">+<span id="LC4086" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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4087
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<pre style="margin: 0;">+<span id="LC4087" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">dcm1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dcm2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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4088
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<pre style="margin: 0;">+<span id="LC4088" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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4089
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<pre style="margin: 0;">+<span id="LC4089" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">dcm1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dcm2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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4090
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<pre style="margin: 0;">+<span id="LC4090" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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4091
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<pre style="margin: 0;">+<span id="LC4091" class="line" lang="cpp"> <span class="p">}</span></span>
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4092
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<pre style="margin: 0;">+<span id="LC4092" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4093
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<pre style="margin: 0;">+<span id="LC4093" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//compareTDCMdimRev()</span></span>
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4094
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<pre style="margin: 0;">+<span id="LC4094" class="line" lang="cpp"></span>
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4052
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4095
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<pre style="margin: 0;"> <span id="LC4095" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif // USING_R</span></span>
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4053
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4096
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<pre style="margin: 0;"> <span id="LC4096" class="line" lang="cpp"></span>
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4054
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4097
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<pre style="margin: 0;"> <span id="LC4097" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="n" style="color: #333;">readDICOMv</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compressFlag</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dti4D</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4064,8 +4107,6 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru</td>
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4064
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4107
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<pre style="margin: 0;"> <span id="LC4107" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">decayFactor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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4065
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4108
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<pre style="margin: 0;"> <span id="LC4108" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">frameDuration</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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4066
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4109
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<pre style="margin: 0;"> <span id="LC4109" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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4067
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<pre style="margin: 0;">-<span id="LC4067" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">repetitionTimeExcitation</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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4068
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<pre style="margin: 0;">-<span id="LC4068" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">repetitionTimeInversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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4069
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4110
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<pre style="margin: 0;"> <span id="LC4110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TVolumeDiffusion</span> <span class="n" style="color: #333;">volDiffusion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">initTVolumeDiffusion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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4070
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4111
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<pre style="margin: 0;"> <span id="LC4111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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4071
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4112
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<pre style="margin: 0;"> <span id="LC4112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4276,6 +4317,8 @@ const uint32_t kEffectiveTE = 0x0018+ (0x9082 << 16);</td>
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4276
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4317
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<pre style="margin: 0;"> <span id="LC4317" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define kTriggerDelayTime 0x0020+uint32_t(0x9153<< 16 ) //FD</span></span>
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4277
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4318
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<pre style="margin: 0;"> <span id="LC4318" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define kDimensionIndexValues 0x0020+uint32_t(0x9157<< 16 ) // UL n-dimensional index of frame.</span></span>
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4278
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<td class="new_line diff-line-num" data-linenumber="4319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4319
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<pre style="margin: 0;"> <span id="LC4319" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define kInStackPositionNumber 0x0020+uint32_t(0x9057<< 16 ) // UL can help determine slices in volume</span></span>
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4320
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<pre style="margin: 0;">+<span id="LC4320" class="line" lang="cpp"></span>
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4321
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<pre style="margin: 0;">+<span id="LC4321" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define kTemporalPositionIndex 0x0020+uint32_t(0x9128<< 16 ) // UL </span></span>
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4279
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4322
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<pre style="margin: 0;"> <span id="LC4322" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define kDimensionIndexPointer 0x0020+uint32_t(0x9165<< 16 )</span></span>
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4280
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4323
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<pre style="margin: 0;"> <span id="LC4323" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//Private Group 21 as Used by Siemens:</span></span>
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4281
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4324
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<pre style="margin: 0;"> <span id="LC4324" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define kSequenceVariant21 0x0021+(0x105B<< 16 )//CS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4424,6 +4467,8 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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4424
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4467
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<pre style="margin: 0;"> <span id="LC4467" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">dimensionIndexPointer</span><span class="p">[</span><span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">];</span></span>
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4425
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4468
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<pre style="margin: 0;"> <span id="LC4468" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">dimensionIndexPointerCounter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4426
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4469
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<pre style="margin: 0;"> <span id="LC4469" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxInStackPositionNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4470
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<pre style="margin: 0;">+<span id="LC4470" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">temporalPositionIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4471
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<pre style="margin: 0;">+<span id="LC4471" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxTemporalPositionIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4427
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4472
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<pre style="margin: 0;"> <span id="LC4472" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//int temporalPositionIdentifier = 0;</span></span>
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4428
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4473
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<pre style="margin: 0;"> <span id="LC4473" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">locationsInAcquisitionPhilips</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4429
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4474
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<pre style="margin: 0;"> <span id="LC4474" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">imagesInAcquisition</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4587,7 +4632,7 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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4587
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4632
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<pre style="margin: 0;"> <span id="LC4632" class="line" lang="cpp"> <span class="n" style="color: #333;">is2005140FSQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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4588
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4633
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<pre style="margin: 0;"> <span id="LC4633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sqDepth</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">sqDepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//should not happen, but protect for faulty anonymization</span></span>
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4589
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4634
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<pre style="margin: 0;"> <span id="LC4634" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if we leave the folder MREchoSequence 0018,9114</span></span>
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4590
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<pre style="margin: 0;">-<span id="LC4590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span> <span class="n" style="color: #333;">nDimIndxVal</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_BRUKER</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_PHILIPS</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sqDepth00189114</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sqDepth</span><span class="p">))</span> <span class="p">{</span></span>
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4635
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<pre style="margin: 0;">+<span id="LC4635" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span> <span class="n" style="color: #333;">nDimIndxVal</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">kMANUFACTURER_CANON</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">manufacturer</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">kMANUFACTURER_BRUKER</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_PHILIPS</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sqDepth00189114</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sqDepth</span><span class="p">))</span> <span class="p">{</span></span>
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4591
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4636
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<pre style="margin: 0;"> <span id="LC4636" class="line" lang="cpp"> <span class="n" style="color: #333;">sqDepth00189114</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//triggered</span></span>
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4592
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4637
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<pre style="margin: 0;"> <span id="LC4637" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("slice %d---> 0020,9157 = %d %d %d\n", inStackPositionNumber, d.dimensionIndexValues[0], d.dimensionIndexValues[1], d.dimensionIndexValues[2]);</span></span>
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4593
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4638
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<pre style="margin: 0;"> <span id="LC4638" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">inStackPositionNumber</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4622,7 +4667,8 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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4622
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4667
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<pre style="margin: 0;"> <span id="LC4667" class="line" lang="cpp"></span>
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4623
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4668
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<pre style="margin: 0;"> <span id="LC4668" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Bruker Enhanced MR IOD: reorder dimensions to ensure InStackPositionNumber corresponds to the first one</span></span>
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4624
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4669
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<pre style="margin: 0;"> <span id="LC4669" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// This will ensure correct ordering of slices in 4D datasets</span></span>
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4625
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<pre style="margin: 0;">-<span id="LC4625" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_BRUKER</span><span class="p">)</span> <span class="p">{</span></span>
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4670
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<pre style="margin: 0;">+<span id="LC4670" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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4671
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<pre style="margin: 0;">+<span id="LC4671" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (d.manufacturer == kMANUFACTURER_BRUKER) {</span></span>
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4626
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4672
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<pre style="margin: 0;"> <span id="LC4672" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for(size_t i = 1; i < dimensionIndexPointerCounter; i++){</span></span>
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4627
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4673
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<pre style="margin: 0;"> <span id="LC4673" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (dimensionIndexPointer[i] == kInStackPositionNumber){</span></span>
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4628
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4674
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<pre style="margin: 0;"> <span id="LC4674" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //swap with first</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4630,8 +4676,9 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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4630
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4676
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<pre style="margin: 0;"> <span id="LC4676" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> dimensionIndexOrder[0] = i;</span></span>
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4631
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4677
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<pre style="margin: 0;"> <span id="LC4677" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4632
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4678
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<pre style="margin: 0;"> <span id="LC4678" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4633
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<pre style="margin: 0;">-<span id="LC4633" class="line" lang="cpp"> <span class="p">}</span></span>
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4679
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<pre style="margin: 0;">+<span id="LC4679" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }<span class="idiff left">*/</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//Canon and Bruker reverse dimensionIndexItem order relative to Philips: new versions introduce compareTDCMdimRev</span></span></span>
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4634
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4680
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<pre style="margin: 0;"> <span id="LC4680" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ndim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nDimIndxVal</span><span class="p">;</span></span>
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4681
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<pre style="margin: 0;">+<span id="LC4681" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("%d: %d %d %d %d\n", ndim, d.dimensionIndexValues[0], d.dimensionIndexValues[1], d.dimensionIndexValues[2], d.dimensionIndexValues[3]);</span></span>
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4635
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4682
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<pre style="margin: 0;"> <span id="LC4682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ndim</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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4636
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4683
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<pre style="margin: 0;"> <span id="LC4683" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;">numDimensionIndexValues</span><span class="p">].</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">dimensionIndexValues</span><span class="p">[</span><span class="n" style="color: #333;">dimensionIndexOrder</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]];</span></span>
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4637
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4684
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<pre style="margin: 0;"> <span id="LC4684" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;">numDimensionIndexValues</span><span class="p">].</span><span class="n" style="color: #333;">TE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TE</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5006,6 +5053,15 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5006
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5053
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<pre style="margin: 0;"> <span id="LC5053" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">compressFlag</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kCompressNone</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">transferSyntax</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.2.840.10008.1.2.4.90"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span></span>
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5007
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5054
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<pre style="margin: 0;"> <span id="LC5054" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">compressionScheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kCompressYes</span><span class="p">;</span></span>
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5008
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5055
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<pre style="margin: 0;"> <span id="LC5055" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("JPEG2000 Lossless support is new: please validate conversion\n");</span></span>
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5056
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<pre style="margin: 0;">+<span id="LC5056" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">transferSyntax</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.2.840.10008.1.2.1.99"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)){</span></span>
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5057
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<pre style="margin: 0;">+<span id="LC5057" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//n.b. Deflate compression applied applies to the encoding of the **entire** DICOM Data Set, not just image data</span></span>
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5058
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<pre style="margin: 0;">+<span id="LC5058" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// see https://www.medicalconnections.co.uk/kb/Transfer-Syntax/</span></span>
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5059
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<pre style="margin: 0;">+<span id="LC5059" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//#ifndef myDisableZLib</span></span>
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5060
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<pre style="margin: 0;">+<span id="LC5060" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//d.compressionScheme = kCompressDeflate;</span></span>
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5061
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<pre style="margin: 0;">+<span id="LC5061" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//#else</span></span>
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5062
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<pre style="margin: 0;">+<span id="LC5062" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Unsupported transfer syntax '%s' (inflate files with 'dcmconv +te gz.dcm raw.dcm' or 'gdcmconv -w gz.dcm raw.dcm)'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">transferSyntax</span><span class="p">);</span></span>
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5063
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<pre style="margin: 0;">+<span id="LC5063" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//abort as invalid (imageStart MUST be >128)</span></span>
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5064
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<pre style="margin: 0;">+<span id="LC5064" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//#endif</span></span>
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5009
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5065
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<pre style="margin: 0;"> <span id="LC5065" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">compressFlag</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kCompressNone</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">transferSyntax</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.2.840.10008.1.2.4.91"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span></span>
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5010
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5066
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<pre style="margin: 0;"> <span id="LC5066" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">compressionScheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kCompressYes</span><span class="p">;</span></span>
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5011
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5067
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<pre style="margin: 0;"> <span id="LC5067" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("JPEG2000 support is new: please validate conversion\n");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5067,6 +5123,8 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5067
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5123
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<pre style="margin: 0;"> <span id="LC5123" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//d.isDerived = true; //this would have 'i- y' skip MoCo images</span></span>
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5068
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5124
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<pre style="margin: 0;"> <span id="LC5124" class="line" lang="cpp"> <span class="n" style="color: #333;">isMoCo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5069
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5125
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<pre style="margin: 0;"> <span id="LC5125" class="line" lang="cpp"> <span class="p">}</span></span>
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5126
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<pre style="margin: 0;">+<span id="LC5126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageType</span><span class="p">,</span> <span class="s" style="color: #d14;">"B0"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageType</span><span class="p">,</span> <span class="s" style="color: #d14;">"MAP"</span><span class="p">))</span></span>
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5127
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<pre style="margin: 0;">+<span id="LC5127" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isRealIsPhaseMapHz</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5070
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5128
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<pre style="margin: 0;"> <span id="LC5128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageType</span><span class="p">,</span> <span class="s" style="color: #d14;">"_ADC_"</span><span class="p">)</span> <span class="p">)</span></span>
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5071
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5129
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<pre style="margin: 0;"> <span id="LC5129" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5072
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5130
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<pre style="margin: 0;"> <span id="LC5130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageType</span><span class="p">,</span> <span class="s" style="color: #d14;">"_TRACEW_"</span><span class="p">)</span> <span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5157,7 +5215,8 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5157
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5215
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<pre style="margin: 0;"> <span id="LC5215" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">modality</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMODALITY_US</span><span class="p">;</span></span>
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5158
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5216
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<pre style="margin: 0;"> <span id="LC5216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5159
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5217
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<pre style="margin: 0;"> <span id="LC5217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kManufacturer</span><span class="p">:</span></span>
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5160
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<pre style="margin: 0;">-<span id="LC5160" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmStrManufacturer</span> <span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">]);</span></span>
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5218
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<pre style="margin: 0;">+<span id="LC5218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_UNKNOWN</span><span class="p">)</span></span>
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5219
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<pre style="margin: 0;">+<span id="LC5219" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmStrManufacturer</span> <span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">]);</span></span>
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5161
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5220
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<pre style="margin: 0;"> <span id="LC5220" class="line" lang="cpp"> <span class="n" style="color: #333;">volDiffusion</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span><span class="p">;</span></span>
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5162
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5221
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<pre style="margin: 0;"> <span id="LC5221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5163
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5222
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<pre style="margin: 0;"> <span id="LC5222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kInstitutionName</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5175,7 +5234,7 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5175
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5234
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<pre style="margin: 0;"> <span id="LC5234" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//issue 256: Philips files report real ComplexImageComponent but Magnitude ImageType https://github.com/rordenlab/dcm2niix/issues/256</span></span>
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5176
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5235
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<pre style="margin: 0;"> <span id="LC5235" class="line" lang="cpp"> <span class="n" style="color: #333;">isPhase</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5177
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5236
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<pre style="margin: 0;"> <span id="LC5236" class="line" lang="cpp"> <span class="n" style="color: #333;">isReal</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5178
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<pre style="margin: 0;">-<span id="LC5178" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">isImaginary</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5237
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<pre style="margin: 0;">+<span id="LC5237" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">isImaginary</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5179
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5238
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<pre style="margin: 0;"> <span id="LC5238" class="line" lang="cpp"> <span class="n" style="color: #333;">isMagnitude</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5180
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5239
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<pre style="margin: 0;"> <span id="LC5239" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//see Table C.8-85 http://dicom.nema.org/medical/Dicom/2017c/output/chtml/part03/sect_C.8.13.3.html</span></span>
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5181
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5240
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<pre style="margin: 0;"> <span id="LC5240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'R'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'E'</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5189,7 +5248,7 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5189
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5248
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<pre style="margin: 0;"> <span id="LC5248" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//not mutually exclusive: possible for Philips enhanced DICOM to store BOTH magnitude and phase in the same image</span></span>
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5190
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5249
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<pre style="margin: 0;"> <span id="LC5249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isPhase</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasPhase</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5191
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5250
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<pre style="margin: 0;"> <span id="LC5250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isReal</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasReal</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5192
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<pre style="margin: 0;">-<span id="LC5192" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isImaginary</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasImaginary</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5251
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<pre style="margin: 0;">+<span id="LC5251" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isImaginary</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasImaginary</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5193
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5252
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<pre style="margin: 0;"> <span id="LC5252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isMagnitude</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasMagnitude</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5194
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5253
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<pre style="margin: 0;"> <span id="LC5253" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5195
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5254
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<pre style="margin: 0;"> <span id="LC5254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kAcquisitionContrast</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5216,7 +5275,8 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5216
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5275
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<pre style="margin: 0;"> <span id="LC5275" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">seriesTimeTxt</span><span class="p">);</span></span>
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5217
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5276
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<pre style="margin: 0;"> <span id="LC5276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> </span>
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5218
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5277
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<pre style="margin: 0;"> <span id="LC5277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kStudyTime</span> <span class="p">:</span></span>
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5219
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<pre style="margin: 0;">-<span id="LC5219" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">studyTime</span><span class="p">);</span></span>
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5278
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<pre style="margin: 0;">+<span id="LC5278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">studyTime</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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5279
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<pre style="margin: 0;">+<span id="LC5279" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">studyTime</span><span class="p">);</span></span>
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5220
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5280
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<pre style="margin: 0;"> <span id="LC5280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5221
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5281
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<pre style="margin: 0;"> <span id="LC5281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kPatientName</span> <span class="p">:</span></span>
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5222
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5282
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<pre style="margin: 0;"> <span id="LC5282" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">patientName</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5293,8 +5353,7 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5293
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5353
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<pre style="margin: 0;"> <span id="LC5353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5294
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5354
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<pre style="margin: 0;"> <span id="LC5354" class="line" lang="cpp"> <span class="p">}</span></span>
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5295
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5355
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<pre style="margin: 0;"> <span id="LC5355" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kProtocolName</span> <span class="p">:</span> <span class="p">{</span></span>
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5296
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<pre style="margin: 0;">-<span id="LC5296" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if ((strlen(d.protocolName) < 1) || (d.manufacturer != kMANUFACTURER_GE)) //GE uses a generic session name here: do not overwrite kProtocolNameGE</span></span>
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5297
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<pre style="margin: 0;">-<span id="LC5297" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//see also kSequenceName</span></span>
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5356
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<pre style="margin: 0;">+<span id="LC5356" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span><span class="p">);</span></span>
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5298
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5357
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<pre style="margin: 0;"> <span id="LC5357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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5299
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5358
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<pre style="margin: 0;"> <span id="LC5358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kPatientOrient</span> <span class="p">:</span></span>
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5300
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5359
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<pre style="margin: 0;"> <span id="LC5359" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">patientOrient</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5563,12 +5622,16 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5563
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5622
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<pre style="margin: 0;"> <span id="LC5622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmStrInt</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">//Philips renames each image again in 2001,9000, which can lead to duplicates</span></span>
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5564
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5623
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<pre style="margin: 0;"> <span id="LC5623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5565
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5624
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<pre style="margin: 0;"> <span id="LC5624" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kInStackPositionNumber</span><span class="p">:</span></span>
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5566
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<pre style="margin: 0;">-<span id="LC5566" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_HITACHI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_UNKNOWN</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_PHILIPS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_BRUKER</span><span class="p">))</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5625
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<pre style="margin: 0;">+<span id="LC5625" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;"><span class="idiff left">kMANUFACTURER_CANON</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">manufacturer</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">kMANUFACTURER_HITACHI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_UNKNOWN</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_PHILIPS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_BRUKER</span><span class="p">))</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="5567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5567
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<td class="new_line diff-line-num" data-linenumber="5626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5626
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<pre style="margin: 0;"> <span id="LC5626" class="line" lang="cpp"> <span class="n" style="color: #333;">inStackPositionNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmInt</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isLittleEndian</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="5568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5568
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<td class="new_line diff-line-num" data-linenumber="5627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5627
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<pre style="margin: 0;"> <span id="LC5627" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (inStackPositionNumber == 1) numInStackPositionNumber1 ++;</span></span>
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5569
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<td class="new_line diff-line-num" data-linenumber="5628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5628
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<pre style="margin: 0;"> <span id="LC5628" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("<%d>\n",inStackPositionNumber);</span></span>
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5570
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<td class="new_line diff-line-num" data-linenumber="5629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5629
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<pre style="margin: 0;"> <span id="LC5629" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">inStackPositionNumber</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxInStackPositionNumber</span><span class="p">)</span> <span class="n" style="color: #333;">maxInStackPositionNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inStackPositionNumber</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="5571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5571
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<td class="new_line diff-line-num" data-linenumber="5630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5630
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<pre style="margin: 0;"> <span id="LC5630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="5572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="5631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5631
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<pre style="margin: 0;">+<span id="LC5631" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kTemporalPositionIndex</span><span class="p">:</span> </span>
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<td class="old_line diff-line-num new" data-linenumber="5572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="5632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5632
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<pre style="margin: 0;">+<span id="LC5632" class="line" lang="cpp"> <span class="n" style="color: #333;">temporalPositionIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmInt</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isLittleEndian</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5633
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<pre style="margin: 0;">+<span id="LC5633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temporalPositionIndex</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxTemporalPositionIndex</span><span class="p">)</span> <span class="n" style="color: #333;">maxTemporalPositionIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temporalPositionIndex</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5634
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<pre style="margin: 0;">+<span id="LC5634" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5572
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<td class="new_line diff-line-num" data-linenumber="5635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5635
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<pre style="margin: 0;"> <span id="LC5635" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kDimensionIndexPointer</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="5573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5573
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<td class="new_line diff-line-num" data-linenumber="5636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5636
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<pre style="margin: 0;"> <span id="LC5636" class="line" lang="cpp"> <span class="n" style="color: #333;">dimensionIndexPointer</span><span class="p">[</span><span class="n" style="color: #333;">dimensionIndexPointerCounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmAttributeTag</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isLittleEndian</span><span class="p">);</span></span>
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5574
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<td class="new_line diff-line-num" data-linenumber="5637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5637
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<pre style="margin: 0;"> <span id="LC5637" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5587,13 +5650,13 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5587
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<td class="new_line diff-line-num" data-linenumber="5650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5650
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<pre style="margin: 0;"> <span id="LC5650" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kDimensionIndexValues</span><span class="p">:</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// kImageNum is not enough for 4D series from Philips 5.*.</span></span>
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<td class="old_line diff-line-num" data-linenumber="5588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5588
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<td class="new_line diff-line-num" data-linenumber="5651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5651
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<pre style="margin: 0;"> <span id="LC5651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5589
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<td class="new_line diff-line-num" data-linenumber="5652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5652
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<pre style="margin: 0;"> <span id="LC5652" class="line" lang="cpp"> <span class="n" style="color: #333;">nDimIndxVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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5590
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<pre style="margin: 0;">-<span id="LC5590" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nDimIndxVal</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">){</span></span>
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5653
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<pre style="margin: 0;">+<span id="LC5653" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nDimIndxVal</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">){</span></span>
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5591
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5654
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<pre style="margin: 0;"> <span id="LC5654" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"%d is too many dimensions. Only up to %d are supported</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nDimIndxVal</span><span class="p">,</span></span>
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5592
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5655
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<pre style="margin: 0;"> <span id="LC5655" class="line" lang="cpp"> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">);</span></span>
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5593
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5656
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<pre style="margin: 0;"> <span id="LC5656" class="line" lang="cpp"> <span class="n" style="color: #333;">nDimIndxVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Truncate</span></span>
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5594
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5657
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<pre style="margin: 0;"> <span id="LC5657" class="line" lang="cpp"> <span class="p">}</span></span>
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5595
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5658
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<pre style="margin: 0;"> <span id="LC5658" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmMultiLongs</span><span class="p">(</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nDimIndxVal</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">nDimIndxVal</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">dimensionIndexValues</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isLittleEndian</span><span class="p">);</span></span>
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5596
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<pre style="margin: 0;">-<span id="LC5596" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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5659
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<pre style="margin: 0;">+<span id="LC5659" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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5597
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5660
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<pre style="margin: 0;"> <span id="LC5660" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kPhotometricInterpretation</span><span class="p">:</span> <span class="p">{</span></span>
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5598
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5661
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<pre style="margin: 0;"> <span id="LC5661" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">interp</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStr</span><span class="p">];</span></span>
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5599
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5662
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<pre style="margin: 0;"> <span id="LC5662" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">interp</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5999,7 +6062,7 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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5999
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6062
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<pre style="margin: 0;"> <span id="LC6062" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Canon/Toshiba omits 0018,9018, but reports [SE\EP];[GR\EP] for 0018,0020</span></span>
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6000
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<td class="new_line diff-line-num" data-linenumber="6063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6063
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<pre style="margin: 0;"> <span id="LC6063" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//GE omits 0018,9018, but reports [EP\GR];[EP\SE] for 0018,0020</span></span>
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6001
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6064
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<pre style="margin: 0;"> <span id="LC6064" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Philips reports 0018,9018, but reports [SE];[GR] for 0018,0020</span></span>
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6002
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<td class="new_line diff-line-num old" data-linenumber="6065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6002" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">scanningSequence</span><span class="p">,</span> <span class="s" style="color: #d14;">"IR"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span></span>
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6065
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<pre style="margin: 0;">+<span id="LC6065" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">scanningSequence</span><span class="p">,</span> <span class="s" style="color: #d14;">"IR"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span></span>
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6003
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6066
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<pre style="margin: 0;"> <span id="LC6066" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6004
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6067
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<pre style="margin: 0;"> <span id="LC6067" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">scanningSequence</span><span class="p">,</span> <span class="s" style="color: #d14;">"EP"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span></span>
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6005
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6068
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<pre style="margin: 0;"> <span id="LC6068" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isEPI</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6014,9 +6077,10 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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6014
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6077
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<pre style="margin: 0;"> <span id="LC6077" class="line" lang="cpp"> <span class="p">}</span></span>
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6015
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6078
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<pre style="margin: 0;"> <span id="LC6078" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kScanOptions</span><span class="p">:</span></span>
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6016
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6079
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<pre style="margin: 0;"> <span id="LC6079" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">scanOptions</span><span class="p">);</span></span>
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6080
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<pre style="margin: 0;">+<span id="LC6080" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">scanOptions</span><span class="p">,</span> <span class="s" style="color: #d14;">"PFF"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6081
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<pre style="margin: 0;">+<span id="LC6081" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isPartialFourier</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//e.g. GE does not populate (0018,9081) </span></span>
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6017
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6082
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<pre style="margin: 0;"> <span id="LC6082" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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6018
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6083
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<pre style="margin: 0;"> <span id="LC6083" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kSequenceName</span> <span class="p">:</span> <span class="p">{</span></span>
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6019
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<pre style="margin: 0;">-<span id="LC6019" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (strlen(d.protocolName) < 1) //precedence given to kProtocolName and kProtocolNameGE</span></span>
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6020
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6084
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<pre style="margin: 0;"> <span id="LC6084" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmStr</span><span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">);</span></span>
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6021
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6085
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<pre style="margin: 0;"> <span id="LC6085" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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6022
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6086
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<pre style="margin: 0;"> <span id="LC6086" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6170,6 +6234,7 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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6170
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6234
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<pre style="margin: 0;"> <span id="LC6234" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//d.CSA.dtiV[3] = v[2];</span></span>
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6171
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6235
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<pre style="margin: 0;"> <span id="LC6235" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("><>< 0018,9089: DWI bxyz %g %g %g %g\n", d.CSA.dtiV[0], d.CSA.dtiV[1], d.CSA.dtiV[2], d.CSA.dtiV[3]);</span></span>
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6172
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6236
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<pre style="margin: 0;"> <span id="LC6236" class="line" lang="cpp"> <span class="n" style="color: #333;">hasDwiDirectionality</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6237
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<pre style="margin: 0;">+<span id="LC6237" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isBVecWorldCoordinates</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//e.g. Canon saved image space coordinates in Comments, world space in 0018, 9089</span></span>
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6173
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<td class="new_line diff-line-num" data-linenumber="6238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6238
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<pre style="margin: 0;"> <span id="LC6238" class="line" lang="cpp"> <span class="n" style="color: #333;">set_orientation0018_9089</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">volDiffusion</span><span class="p">,</span> <span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">lPos</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isLittleEndian</span><span class="p">);</span></span>
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6174
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6239
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<pre style="margin: 0;"> <span id="LC6239" class="line" lang="cpp"> <span class="p">}</span></span>
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6175
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6240
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<pre style="margin: 0;"> <span id="LC6240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6708,9 +6773,6 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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6708
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6773
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<pre style="margin: 0;"> <span id="LC6773" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//printMessage(" tag=%04x,%04x length=%u pos=%ld %c%c nest=%d\n", groupElement & 65535,groupElement>>16, lLength, lPos,vr[0], vr[1], nest);</span></span>
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6709
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6774
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<pre style="margin: 0;"> <span id="LC6774" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6710
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6775
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<pre style="margin: 0;"> <span id="LC6775" class="line" lang="cpp"> <span class="n" style="color: #333;">lPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">);</span></span>
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6711
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<pre style="margin: 0;">-<span id="LC6711" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("%d\n",d.imageStart);</span></span>
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6712
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<pre style="margin: 0;">-<span id="LC6712" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage(" DWI bxyz %g %g %g %g %d\n", d.CSA.dtiV[0], d.CSA.dtiV[1], d.CSA.dtiV[2], d.CSA.dtiV[3], d.CSA.numDti);</span></span>
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6713
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<pre style="margin: 0;">-<span id="LC6713" class="line" lang="cpp"></span>
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6714
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6776
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<pre style="margin: 0;"> <span id="LC6776" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//while d.imageStart == 0</span></span>
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6715
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6777
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<pre style="margin: 0;"> <span id="LC6777" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span> <span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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6716
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6778
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<pre style="margin: 0;"> <span id="LC6778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">bitsStored</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isValid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6841,8 +6903,14 @@ uint32_t kSequenceDelimitationItemTag = 0xFFFE +(0xE0DD << 16 );</td>
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6841
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6903
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<pre style="margin: 0;"> <span id="LC6903" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"0008,0008=MOSAIC but number of slices not specified: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">);</span></span>
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6842
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6904
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<pre style="margin: 0;"> <span id="LC6904" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_SIEMENS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">dtiV</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">dtiV</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">dtiV</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">))</span></span>
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6843
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6905
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<pre style="margin: 0;"> <span id="LC6905" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">dtiV</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//SiemensTrio-Syngo2004A reports B=0 images as having impossible b-vectors.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6844
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<td class="new_line diff-line-num old" data-linenumber="6906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6844" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_GE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">modality</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMODALITY_MR</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesDescription</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;">//GE uses a generic session name here: do not overwrite kProtocolNameGE</span></span>
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6906
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<pre style="margin: 0;">+<span id="LC6906" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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6907
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<pre style="margin: 0;">+<span id="LC6907" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((d.manufacturer == kMANUFACTURER_GE) && (d.modality == kMODALITY_MR) && (strlen(d.seriesDescription) > 1)) {</span></span>
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6908
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<pre style="margin: 0;">+<span id="LC6908" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //issue 473, 476: swap protocolName and seriesDescription</span></span>
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6909
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<pre style="margin: 0;">+<span id="LC6909" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> char tempTxt[kDICOMStr] = "";</span></span>
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6910
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<pre style="margin: 0;">+<span id="LC6910" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> strcpy(tempTxt, d.protocolName);</span></span>
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6845
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6911
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<pre style="margin: 0;"> <span id="LC6911" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> strcpy(d.protocolName, d.seriesDescription);</span></span>
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6912
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<pre style="margin: 0;">+<span id="LC6912" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> strcpy(d.seriesDescription, tempTxt);</span></span>
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6913
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<pre style="margin: 0;">+<span id="LC6913" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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6846
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6914
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<pre style="margin: 0;"> <span id="LC6914" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesDescription</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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6847
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6915
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<pre style="margin: 0;"> <span id="LC6915" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesDescription</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="6848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6848
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6916
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<pre style="margin: 0;"> <span id="LC6916" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">isMoCo</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6901,7 +6969,6 @@ if (d.isHasPhase)</td>
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6901
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<td class="new_line diff-line-num" data-linenumber="6969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6969
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<pre style="margin: 0;"> <span id="LC6969" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">patientPositionStartPhilips</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span> <span class="c1" style="color: #998; font-style: italic;">//for Philips data without</span></span>
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<td class="old_line diff-line-num" data-linenumber="6902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6902
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6970
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<pre style="margin: 0;"> <span id="LC6970" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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6903
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6971
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<pre style="margin: 0;"> <span id="LC6971" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">patientPosition</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">patientPositionStartPhilips</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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6904
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<td class="new_line diff-line-num old" data-linenumber="6972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6904" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("%d %g\n", d.imageNum, sliceLocation); //shame this tag is optional</span></span>
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6905
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6972
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<pre style="margin: 0;"> <span id="LC6972" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isVerbose</span><span class="p">)</span> <span class="p">{</span></span>
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6906
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6973
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<pre style="margin: 0;"> <span id="LC6973" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"DICOM file: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">);</span></span>
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6907
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<td class="new_line diff-line-num" data-linenumber="6974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6974
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<pre style="margin: 0;"> <span id="LC6974" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" patient position (0020,0032)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%g</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%g</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%g</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">patientPosition</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">patientPosition</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">patientPosition</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6958,9 +7025,10 @@ if (d.isHasPhase)</td>
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<td class="old_line diff-line-num" data-linenumber="6958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6958
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<td class="new_line diff-line-num" data-linenumber="7025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7025
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<pre style="margin: 0;"> <span id="LC7025" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// printWarning("3D EPI with FrameAcquisitionDuration = %gs volumes = %d (see issue 369)\n", frameAcquisitionDuration/1000.0, d.xyzDim[4]);</span></span>
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6959
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<td class="new_line diff-line-num" data-linenumber="7026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7026
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<pre style="margin: 0;"> <span id="LC7026" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numDimensionIndexValues</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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6960
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<td class="new_line diff-line-num" data-linenumber="7027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7027
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<pre style="margin: 0;"> <span id="LC7027" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageType</span><span class="p">,</span> <span class="n" style="color: #333;">imageType1st</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//for multi-frame datasets, return name of book, not name of last chapter</span></span>
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6961
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<pre style="margin: 0;">-<span id="LC6961" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">numDimensionIndexValues</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">numDimensionIndexValues</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">))</span> <span class="p">{</span></span>
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7028
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<pre style="margin: 0;">+<span id="LC7028" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">numDimensionIndexValues</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">numDimensionIndexValues</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">))</span> <span class="p">{</span></span>
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6962
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7029
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<pre style="margin: 0;"> <span id="LC7029" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Philips enhanced datasets can have custom slice orders and pack images with different TE, Phase/Magnitude/Etc.</span></span>
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6963
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<pre style="margin: 0;">-<span id="LC6963" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isVerbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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7030
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<pre style="margin: 0;">+<span id="LC7030" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxVariableItem</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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7031
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<pre style="margin: 0;">+<span id="LC7031" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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6964
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7032
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<pre style="margin: 0;"> <span id="LC7032" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mn</span><span class="p">[</span><span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">];</span></span>
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6965
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7033
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<pre style="margin: 0;"> <span id="LC7033" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mx</span><span class="p">[</span><span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">];</span></span>
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6966
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7034
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<pre style="margin: 0;"> <span id="LC7034" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6970,20 +7038,35 @@ if (d.isHasPhase)</td>
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6970
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7038
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<pre style="margin: 0;"> <span id="LC7038" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="n" style="color: #333;">mx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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6971
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7039
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<pre style="margin: 0;"> <span id="LC7039" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mn</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="n" style="color: #333;">mn</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">dimIdx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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6972
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7040
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<pre style="margin: 0;"> <span id="LC7040" class="line" lang="cpp"> <span class="p">}</span></span>
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7041
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<pre style="margin: 0;">+<span id="LC7041" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">mn</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="n" style="color: #333;">maxVariableItem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span> </span>
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6973
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7042
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<pre style="margin: 0;"> <span id="LC7042" class="line" lang="cpp"> <span class="p">}</span></span>
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6974
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<td class="new_line diff-line-num old" data-linenumber="7043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6974" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" DimensionIndexValues (0020,9157), dimensions with variability:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6975
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<pre style="margin: 0;">-<span id="LC6975" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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6976
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<pre style="margin: 0;">-<span id="LC6976" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">mx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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6977
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<pre style="margin: 0;">-<span id="LC6977" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" Dimension %d Range: %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">mn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">mx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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7043
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<pre style="margin: 0;">+<span id="LC7043" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isVerbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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7044
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<pre style="margin: 0;">+<span id="LC7044" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" DimensionIndexValues (0020,9157), dimensions with variability:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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7045
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<pre style="margin: 0;">+<span id="LC7045" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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7046
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<pre style="margin: 0;">+<span id="LC7046" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">mx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> </span>
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7047
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<pre style="margin: 0;">+<span id="LC7047" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" Dimension %d Range: %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">mn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">mx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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7048
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<pre style="margin: 0;">+<span id="LC7048" class="line" lang="cpp"> <span class="p">}</span></span>
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6978
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7049
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<pre style="margin: 0;"> <span id="LC7049" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//verbose > 1</span></span>
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7050
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<pre style="margin: 0;">+<span id="LC7050" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//see http://dicom.nema.org/medical/Dicom/2018d/output/chtml/part03/sect_C.8.24.3.3.html</span></span>
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7051
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<pre style="margin: 0;">+<span id="LC7051" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Philips puts spatial position as lower item than temporal position, the reverse is true for Bruker and Canon</span></span>
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7052
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<pre style="margin: 0;">+<span id="LC7052" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stackPositionItem</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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7053
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<pre style="margin: 0;">+<span id="LC7053" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dimensionIndexPointerCounter</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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7054
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<pre style="margin: 0;">+<span id="LC7054" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dimensionIndexPointerCounter</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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7055
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<pre style="margin: 0;">+<span id="LC7055" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dimensionIndexPointer</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kInStackPositionNumber</span><span class="p">)</span> <span class="n" style="color: #333;">stackPositionItem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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6979
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7056
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<pre style="margin: 0;"> <span id="LC7056" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//sort dimensions</span></span>
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6980
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7057
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<pre style="margin: 0;"> <span id="LC7057" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USING_R</span></span>
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6981
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<pre style="margin: 0;">-<span id="LC6981" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">dcmDim</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">,</span> <span class="n" style="color: #333;">compareTDCMdim</span><span class="p">);</span></span>
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7058
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<pre style="margin: 0;">+<span id="LC7058" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stackPositionItem</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxVariableItem</span><span class="p">)</span></span>
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7059
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<pre style="margin: 0;">+<span id="LC7059" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">dcmDim</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">,</span> <span class="n" style="color: #333;">compareTDCMdim</span><span class="p">);</span></span>
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7060
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<pre style="margin: 0;">+<span id="LC7060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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7061
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<pre style="margin: 0;">+<span id="LC7061" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">dcmDim</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">,</span> <span class="n" style="color: #333;">compareTDCMdimRev</span><span class="p">);</span></span>
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6982
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7062
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<pre style="margin: 0;"> <span id="LC7062" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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6983
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<pre style="margin: 0;">-<span id="LC6983" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmDim</span><span class="p">,</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span><span class="p">),</span> <span class="n" style="color: #333;">compareTDCMdim</span><span class="p">);</span></span>
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7063
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<pre style="margin: 0;">+<span id="LC7063" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stackPositionItem</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxVariableItem</span><span class="p">)</span></span>
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7064
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<pre style="margin: 0;">+<span id="LC7064" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmDim</span><span class="p">,</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span><span class="p">),</span> <span class="n" style="color: #333;">compareTDCMdim</span><span class="p">);</span></span>
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7065
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<pre style="margin: 0;">+<span id="LC7065" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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7066
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<pre style="margin: 0;">+<span id="LC7066" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmDim</span><span class="p">,</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMdim</span><span class="p">),</span> <span class="n" style="color: #333;">compareTDCMdimRev</span><span class="p">);</span></span>
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6984
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7067
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<pre style="margin: 0;"> <span id="LC7067" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6985
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7068
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<pre style="margin: 0;"> <span id="LC7068" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for (int i = 0; i < numberOfFrames; i++)</span></span>
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6986
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<pre style="margin: 0;">-<span id="LC6986" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// printf("diskPos= %d dimIdx= %d %d %d %d TE= %g\n", i, dcmDim[i].diskPos, dcmDim[i].dimIdx[1], dcmDim[i].dimIdx[2], dcmDim[i].dimIdx[3], dti4D->TE[i]);</span></span>
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7069
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<pre style="margin: 0;">+<span id="LC7069" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// printf("<span class="idiff left">i %d </span>diskPos= %d dimIdx= %d %d %d %d TE= %g\n", i, dcmDim[i].diskPos, <span class="idiff right">dcmDim[i].dimIdx[0], </span>dcmDim[i].dimIdx[1], dcmDim[i].dimIdx[2], dcmDim[i].dimIdx[3], dti4D->TE[i]);</span></span>
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6987
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7070
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<pre style="margin: 0;"> <span id="LC7070" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numberOfFrames</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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6988
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7071
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<pre style="margin: 0;"> <span id="LC7071" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sliceOrder</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">diskPos</span><span class="p">;</span></span>
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6989
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7072
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<pre style="margin: 0;"> <span id="LC7072" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">intenScale</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7003,29 +7086,31 @@ if (d.isHasPhase)</td>
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7003
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7086
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<pre style="margin: 0;"> <span id="LC7086" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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7004
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7087
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<pre style="margin: 0;"> <span id="LC7087" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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7005
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7088
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<pre style="margin: 0;"> <span id="LC7088" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC7089" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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7006
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7090
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<pre style="margin: 0;"> <span id="LC7090" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//dti4D->gradDynVol[i] = 0; //only PAR/REC</span></span>
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7007
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<pre style="margin: 0;">-<span id="LC7007" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">TE</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">TE</span><span class="p">;</span></span>
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7008
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<pre style="margin: 0;">-<span id="LC7008" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isPhase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">isPhase</span><span class="p">;</span></span>
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7009
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<pre style="margin: 0;">-<span id="LC7009" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isReal</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">isReal</span><span class="p">;</span></span>
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7010
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<pre style="margin: 0;">-<span id="LC7010" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isImaginary</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">isImaginary</span><span class="p">;</span></span>
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7011
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<pre style="margin: 0;">-<span id="LC7011" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">triggerDelayTime</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">triggerDelayTime</span><span class="p">;</span></span>
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7012
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<pre style="margin: 0;">-<span id="LC7012" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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7013
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<pre style="margin: 0;">-<span id="LC7013" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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7014
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<pre style="margin: 0;">-<span id="LC7014" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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7015
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<pre style="margin: 0;">-<span id="LC7015" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xyzDim</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">])</span>].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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7091
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<pre style="margin: 0;">+<span id="LC7091" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">TE</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">TE</span><span class="p">;</span></span>
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7092
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<pre style="margin: 0;">+<span id="LC7092" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isPhase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">isPhase</span><span class="p">;</span></span>
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7093
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<pre style="margin: 0;">+<span id="LC7093" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isReal</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">isReal</span><span class="p">;</span></span>
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7094
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<pre style="margin: 0;">+<span id="LC7094" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isImaginary</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">isImaginary</span><span class="p">;</span></span>
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7095
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<pre style="margin: 0;">+<span id="LC7095" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">triggerDelayTime</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">triggerDelayTime</span><span class="p">;</span></span>
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7096
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<pre style="margin: 0;">+<span id="LC7096" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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7097
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<pre style="margin: 0;">+<span id="LC7097" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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7098
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<pre style="margin: 0;">+<span id="LC7098" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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7099
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<pre style="margin: 0;">+<span id="LC7099" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmDim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">slice</span></span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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7016
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<td class="new_line diff-line-num" data-linenumber="7100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7100
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<pre style="margin: 0;"> <span id="LC7100" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("te=\t%g\tscl=\t%g\tintercept=\t%g\n",dti4D->TE[i], dti4D->intenScale[i],dti4D->intenIntercept[i]);</span></span>
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7017
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<td class="new_line diff-line-num" data-linenumber="7101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7101
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<pre style="margin: 0;"> <span id="LC7101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">TE</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">TE</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">TE</span><span class="p">))</span> <span class="n" style="color: #333;">isTEvaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7018
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<td class="new_line diff-line-num" data-linenumber="7102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7102
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<pre style="margin: 0;"> <span id="LC7102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isPhase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">isPhase</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isScaleOrTEVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7019
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<td class="new_line diff-line-num" data-linenumber="7103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7103
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<pre style="margin: 0;"> <span id="LC7103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">triggerDelayTime</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">triggerDelayTime</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isScaleOrTEVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7020
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<td class="new_line diff-line-num" data-linenumber="7104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7104
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<pre style="margin: 0;"> <span id="LC7104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isReal</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">isReal</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isScaleOrTEVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7021
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<td class="new_line diff-line-num" data-linenumber="7105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7105
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<pre style="margin: 0;"> <span id="LC7105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isImaginary</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">isImaginary</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isScaleOrTEVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7022
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<td class="new_line diff-line-num old" data-linenumber="7106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7022" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//dti4D->intenScale[i] = dcmDim[j+(i * d.xyzDim[3])].intenScale;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7023
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<td class="new_line diff-line-num old" data-linenumber="7106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7023" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//dti4D->intenIntercept[i] = dcmDim[j+(i * d.xyzDim[3])].intenIntercept;</span></span>
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7024
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<pre style="margin: 0;">-<span id="LC7024" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//dti4D->intenScalePhilips[i] = dcmDim[j+(i * d.xyzDim[3])].intenScalePhilips;</span></span>
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7025
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<pre style="margin: 0;">-<span id="LC7025" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//dti4D->RWVIntercept[i] = dcmDim[j+(i * d.xyzDim[3])].RWVIntercept;</span></span>
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7026
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<pre style="margin: 0;">-<span id="LC7026" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//dti4D->RWVScale[i] = dcmDim[j+(i * d.xyzDim[3])].RWVScale;</span></span>
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7027
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<pre style="margin: 0;">-<span id="LC7027" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (dti4D->intenScale[i] != d.intenScale) isScaleVaries = true;</span></span>
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7028
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<pre style="margin: 0;">-<span id="LC7028" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (dti4D->intenIntercept[i] != d.intenIntercept) isScaleVaries = true;</span></span>
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7106
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<pre style="margin: 0;">+<span id="LC7106" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*Philips can vary intensity scalings for separate slices within a volume!</span></span>
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7107
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<pre style="margin: 0;">+<span id="LC7107" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> dti4D->intenScale[i] = dcmDim[slice].intenScale;</span></span>
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7108
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<pre style="margin: 0;">+<span id="LC7108" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> dti4D->intenIntercept[i] = dcmDim[slice].intenIntercept;</span></span>
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7109
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<pre style="margin: 0;">+<span id="LC7109" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> dti4D->intenScalePhilips[i] = dcmDim[slice].intenScalePhilips;</span></span>
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7110
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<pre style="margin: 0;">+<span id="LC7110" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> dti4D->RWVIntercept[i] = dcmDim[slice].RWVIntercept;</span></span>
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7111
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<pre style="margin: 0;">+<span id="LC7111" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> dti4D->RWVScale[i] = dcmDim[slice].RWVScale;</span></span>
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7112
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<pre style="margin: 0;">+<span id="LC7112" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (dti4D->intenScale[i] != d.intenScale) isScaleVaries = true;</span></span>
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7113
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<pre style="margin: 0;">+<span id="LC7113" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (dti4D->intenIntercept[i] != d.intenIntercept) isScaleVaries = true;*/</span></span>
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7029
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7114
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<pre style="margin: 0;"> <span id="LC7114" class="line" lang="cpp"> <span class="p">}</span></span>
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7030
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7115
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<pre style="margin: 0;"> <span id="LC7115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">isScaleVaries</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">isTEvaries</span><span class="p">))</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isScaleOrTEVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7031
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7116
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<pre style="margin: 0;"> <span id="LC7116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isTEvaries</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isMultiEcho</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7036,8 +7121,10 @@ if (d.isHasPhase)</td>
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7036
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7121
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<pre style="margin: 0;"> <span id="LC7121" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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7037
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7122
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<pre style="margin: 0;"> <span id="LC7122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isVerbose</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isScaleOrTEVaries</span><span class="p">))</span> <span class="p">{</span></span>
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7038
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7123
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<pre style="margin: 0;"> <span id="LC7123" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Parameters vary across 3D volumes packed in single DICOM file:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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7039
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<pre style="margin: 0;">-<span id="LC7039" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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7040
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<pre style="margin: 0;">-<span id="LC7040" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" %d TE=%g Slope=%g Inter=%g PhilipsScale=%g Phase=%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">TE</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenIntercept</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isPhase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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7124
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<pre style="margin: 0;">+<span id="LC7124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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7125
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<pre style="margin: 0;">+<span id="LC7125" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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7126
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<pre style="margin: 0;">+<span id="LC7126" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">" %d TE=%g Slope=%g Inter=%g PhilipsScale=%g Phase=%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">TE</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="n" style="color: #333;">slice</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenIntercept</span><span class="p">[</span><span class="n" style="color: #333;">slice</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">[</span><span class="n" style="color: #333;">slice</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isPhase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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7127
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<pre style="margin: 0;">+<span id="LC7127" class="line" lang="cpp"> <span class="p">}</span></span>
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7041
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7128
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<pre style="margin: 0;"> <span id="LC7128" class="line" lang="cpp"> <span class="p">}</span></span>
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7042
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7129
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<pre style="margin: 0;"> <span id="LC7129" class="line" lang="cpp"> <span class="p">}</span></span>
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7043
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7130
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<pre style="margin: 0;"> <span id="LC7130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">maxInStackPositionNumber</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">maxInStackPositionNumber</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">zSpacing</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7121,7 +7208,7 @@ if (d.isHasPhase)</td>
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7121
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7208
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<pre style="margin: 0;"> <span id="LC7208" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">triggerDelayTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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7122
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7209
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<pre style="margin: 0;"> <span id="LC7209" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("%d\t%g\t%g\t%g\n", d.imageNum, d.acquisitionTime, d.triggerDelayTime, MRImageDynamicScanBeginTime);</span></span>
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7123
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<td class="new_line diff-line-num" data-linenumber="7210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7210
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<pre style="margin: 0;"> <span id="LC7210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_SIEMENS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">seriesTimeTxt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isXA10A</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="p">{</span></span>
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7124
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<pre style="margin: 0;">-<span id="LC7124" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printWarning("Ignoring series number of XA data saved as classic DICOM (issue 394)\n");</span></span>
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7211
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<pre style="margin: 0;">+<span id="LC7211" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printWarning("<span class="idiff left right">>></span>Ignoring series number of XA data saved as classic DICOM (issue 394)\n");</span></span>
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7125
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<td class="new_line diff-line-num" data-linenumber="7212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7212
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<pre style="margin: 0;"> <span id="LC7212" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isStackableSeries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7126
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<td class="new_line diff-line-num" data-linenumber="7213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7213
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<pre style="margin: 0;"> <span id="LC7213" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1000</span><span class="p">);</span></span>
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7127
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<td class="new_line diff-line-num" data-linenumber="7214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7214
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<pre style="margin: 0;"> <span id="LC7214" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesInstanceUID</span><span class="p">,</span> <span class="n" style="color: #333;">seriesTimeTxt</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// dest <- src</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7169,7 +7256,7 @@ if (d.isHasPhase)</td>
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7169
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7256
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<pre style="margin: 0;"> <span id="LC7256" class="line" lang="cpp"> <span class="p">}</span></span>
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7170
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7257
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<pre style="margin: 0;"> <span id="LC7257" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesUidCrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mz_crc32X</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesInstanceUID</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">seriesInstanceUID</span><span class="p">));</span></span>
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7171
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7258
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<pre style="margin: 0;"> <span id="LC7258" class="line" lang="cpp"> <span class="p">}</span></span>
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7172
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<td class="new_line diff-line-num old" data-linenumber="7259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7172" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_SIEMENS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="s" style="color: #d14;">"fl2d1"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="7173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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7259
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<pre style="margin: 0;">+<span id="LC7259" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_SIEMENS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="s" style="color: #d14;">"fl2d1"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span> <span class="p">{</span></span>
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7173
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7260
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<pre style="margin: 0;"> <span id="LC7260" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isLocalizer</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="7174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7174
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7261
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<pre style="margin: 0;"> <span id="LC7261" class="line" lang="cpp"> <span class="p">}</span></span>
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7175
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7262
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<pre style="margin: 0;"> <span id="LC7262" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//UIH 3D T1 scans report echo train length, which is interpreted as 3D EPI</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7230,7 +7317,9 @@ if (d.isHasPhase)</td>
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7230
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7317
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<pre style="margin: 0;"> <span id="LC7317" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// readDICOM()</span></span>
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<td class="old_line diff-line-num" data-linenumber="7231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7231
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7318
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<pre style="margin: 0;"> <span id="LC7318" class="line" lang="cpp"></span>
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7232
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<td class="new_line diff-line-num" data-linenumber="7319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7319
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<pre style="margin: 0;"> <span id="LC7319" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="n" style="color: #333;">readDICOM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fname</span><span class="p">)</span> <span class="p">{</span></span>
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7233
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<td class="new_line diff-line-num old" data-linenumber="7320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7233" class="line" lang="cpp"> <span class="n" style="color: #333;">TDTI4D</span> <span class="n" style="color: #333;">unused</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7234
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<td class="new_line diff-line-num old" data-linenumber="7320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">readDICOMv</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">kCompressSupport</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">unused</span><span class="p">);</span></span>
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7320
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<pre style="margin: 0;">+<span id="LC7320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dti4D</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//unused</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7321
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<pre style="margin: 0;">+<span id="LC7321" class="line" lang="cpp"> <span class="n" style="color: #333;">TDICOMdata</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDICOMv</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">kCompressSupport</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7322
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<pre style="margin: 0;">+<span id="LC7322" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7323
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<pre style="margin: 0;">+<span id="LC7323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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7235
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7324
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<pre style="margin: 0;"> <span id="LC7324" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// readDICOM()</span></span>
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<pre style="margin: 0;"> <span id="LC7325" class="line" lang="cpp"></span></pre>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#dec6a857028e619f96c0e3ba3e43dfdc5bce1b7f"><strong>console/nii_dicom.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,18 +44,18 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if defined(__arm__) || defined(__ARM_ARCH)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="cp" style="color: #999; font-weight: 600;">#define kCPUsuf " ARM" </span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#elif defined(__x86_64)<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#elif defined(__x86_64)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="cp" style="color: #999; font-weight: 600;">#define kCPUsuf " x86-64"</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="cp" style="color: #999; font-weight: 600;">#define kCPUsuf " " //unknown CPU</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define kDCMdate "v1.0.202<span class="idiff left right">01102</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define kDCMdate "v1.0.202<span class="idiff left right">10317</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kMaxEPI3D</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//maximum number of EPI images in Siemens Mosaic</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kMax<span class="idiff left">DTI4D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">18000</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">//maximum number of DTI directions for 4D (Philips) images, also</span> maximum number of <span class="idiff">3</span>D slices <span class="idiff right">for Philips 3D and 4D</span> images</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kMax<span class="idiff left">Slice2D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">64000</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//maximum number of 2D slices in 4D (Philips) images</span></span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kMax<span class="idiff left">Slice2D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">65535</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">//issue460</span> maximum number of <span class="idiff">2</span>D slices <span class="idiff right">in 4D (Philips)</span> images</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kMax<span class="idiff left">DTI4D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kMaxSlice2D</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//issue460: maximum number of DTI directions for 4D (Philips) images, also maximum number of 2D slices for Enhanced DICOM and PAR/REC</span></span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define kDICOMStr 66 //64 characters plus NULL https://github.com/rordenlab/dcm2niix/issues/268</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define kDICOMStrLarge 256</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,7 +139,7 @@ static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;</td>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isReal</span><span class="p">[</span><span class="n" style="color: #333;">kMaxDTI4D</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isImaginary</span><span class="p">[</span><span class="n" style="color: #333;">kMaxDTI4D</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isPhase</span><span class="p">[</span><span class="n" style="color: #333;">kMaxDTI4D</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">repetitionTimeExcitation</span><span class="p">,</span> <span class="n" style="color: #333;">repetitionTimeInversion</span><span class="p">;</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">repetitionTimeExcitation</span><span class="p">,</span> <span class="n" style="color: #333;">repetitionTimeInversion</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _MSC_VER //Microsoft nomenclature for packed structures is different...</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -192,7 +192,7 @@ static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;</td>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">institutionAddress</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">],</span> <span class="n" style="color: #333;">imageComments</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">dimensionIndexValues</span><span class="p">[</span><span class="n" style="color: #333;">MAX_NUMBER_OF_DIMENSIONS</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">TCSAdata</span> <span class="n" style="color: #333;">CSA</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isPrivateCreatorRemap</span><span class="p">,</span> <span class="n" style="color: #333;">isHasOverlay</span><span class="p">,</span> <span class="n" style="color: #333;">isEPI</span><span class="p">,</span> <span class="n" style="color: #333;">isIR</span><span class="p">,</span> <span class="n" style="color: #333;">isPartialFourier</span><span class="p">,</span> <span class="n" style="color: #333;">isDiffusion</span><span class="p">,</span> <span class="n" style="color: #333;">isVectorFromBMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">isRawDataStorage</span><span class="p">,</span> <span class="n" style="color: #333;">isGrayscaleSoftcopyPresentationState</span><span class="p">,</span> <span class="n" style="color: #333;">isStackableSeries</span><span class="p">,</span> <span class="n" style="color: #333;">isCoilVaries</span><span class="p">,</span> <span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">,</span> <span class="n" style="color: #333;">isSegamiOasis</span><span class="p">,</span> <span class="n" style="color: #333;">isXA10A</span><span class="p">,</span> <span class="n" style="color: #333;">isScaleOrTEVaries</span><span class="p">,</span> <span class="n" style="color: #333;">isScaleVariesEnh</span><span class="p">,</span> <span class="n" style="color: #333;">isDerived</span><span class="p">,</span> <span class="n" style="color: #333;">isXRay</span><span class="p">,</span> <span class="n" style="color: #333;">isMultiEcho</span><span class="p">,</span> <span class="n" style="color: #333;">isValid</span><span class="p">,</span> <span class="n" style="color: #333;">is3DAcq</span><span class="p">,</span> <span class="n" style="color: #333;">is2DAcq</span><span class="p">,</span> <span class="n" style="color: #333;">isExplicitVR</span><span class="p">,</span> <span class="n" style="color: #333;">isLittleEndian</span><span class="p">,</span> <span class="n" style="color: #333;">isPlanarRGB</span><span class="p">,</span> <span class="n" style="color: #333;">isSigned</span><span class="p">,</span> <span class="n" style="color: #333;">isHasPhase</span><span class="p">,</span> <span class="n" style="color: #333;">isHasImaginary</span><span class="p">,</span> <span class="n" style="color: #333;">isHasReal</span><span class="p">,</span> <span class="n" style="color: #333;">isHasMagnitude</span><span class="p">,</span><span class="n" style="color: #333;">isHasMixed</span><span class="p">,</span> <span class="n" style="color: #333;">isFloat</span><span class="p">,</span> <span class="n" style="color: #333;">isResampled</span><span class="p">,</span> <span class="n" style="color: #333;">isLocalizer</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;"><span class="idiff left">isRealIsPhaseMapHz</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;">isPrivateCreatorRemap</span><span class="p">,</span> <span class="n" style="color: #333;">isHasOverlay</span><span class="p">,</span> <span class="n" style="color: #333;">isEPI</span><span class="p">,</span> <span class="n" style="color: #333;">isIR</span><span class="p">,</span> <span class="n" style="color: #333;">isPartialFourier</span><span class="p">,</span> <span class="n" style="color: #333;">isDiffusion</span><span class="p">,</span> <span class="n" style="color: #333;">isVectorFromBMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">isRawDataStorage</span><span class="p">,</span> <span class="n" style="color: #333;">isGrayscaleSoftcopyPresentationState</span><span class="p">,</span> <span class="n" style="color: #333;">isStackableSeries</span><span class="p">,</span> <span class="n" style="color: #333;">isCoilVaries</span><span class="p">,</span> <span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">isBVecWorldCoordinates</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">isSegamiOasis</span><span class="p">,</span> <span class="n" style="color: #333;">isXA10A</span><span class="p">,</span> <span class="n" style="color: #333;">isScaleOrTEVaries</span><span class="p">,</span> <span class="n" style="color: #333;">isScaleVariesEnh</span><span class="p">,</span> <span class="n" style="color: #333;">isDerived</span><span class="p">,</span> <span class="n" style="color: #333;">isXRay</span><span class="p">,</span> <span class="n" style="color: #333;">isMultiEcho</span><span class="p">,</span> <span class="n" style="color: #333;">isValid</span><span class="p">,</span> <span class="n" style="color: #333;">is3DAcq</span><span class="p">,</span> <span class="n" style="color: #333;">is2DAcq</span><span class="p">,</span> <span class="n" style="color: #333;">isExplicitVR</span><span class="p">,</span> <span class="n" style="color: #333;">isLittleEndian</span><span class="p">,</span> <span class="n" style="color: #333;">isPlanarRGB</span><span class="p">,</span> <span class="n" style="color: #333;">isSigned</span><span class="p">,</span> <span class="n" style="color: #333;">isHasPhase</span><span class="p">,</span> <span class="n" style="color: #333;">isHasImaginary</span><span class="p">,</span> <span class="n" style="color: #333;">isHasReal</span><span class="p">,</span> <span class="n" style="color: #333;">isHasMagnitude</span><span class="p">,</span><span class="n" style="color: #333;">isHasMixed</span><span class="p">,</span> <span class="n" style="color: #333;">isFloat</span><span class="p">,</span> <span class="n" style="color: #333;">isResampled</span><span class="p">,</span> <span class="n" style="color: #333;">isLocalizer</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">phaseEncodingRC</span><span class="p">,</span> <span class="n" style="color: #333;">patientSex</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"> <span class="p">};</span></span>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#ef8e48ac088b20316ce9b8a7853d81ba9b64f51b"><strong>console/nii_dicom_batch.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,11 +57,9 @@</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(_WIN64) || defined(_WIN32)</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define myTextFileInputLists //comment out to disable this feature: https://github.com/rordenlab/dcm2niix/issues/288</span></span>
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61
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">kPathSeparator</span> <span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'\\'</span><span class="p">;</span></span>
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62
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">kFileSep</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define myTextFileInputLists</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">kPathSeparator</span> <span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'/'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">kFileSep</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/"</span><span class="p">;</span></span>
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67
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -190,6 +188,8 @@ void geCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx, int isV</td>
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190
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//COL then if swap the x and y value and reverse the sign on the z value.</span></span>
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191
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//If the phase encoding is not COL, then just reverse the sign on the x value.</span></span>
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192
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_GE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_CANON</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isBVecWorldCoordinates</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Canon classic DICOMs use image space, enhanced use world space!</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isEPI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//issue449</span></span>
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193
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patientOrient</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'H'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patientOrient</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'F'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patientOrient</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'S'</span><span class="p">))</span></span>
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195
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//participant was head first supine</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -205,7 +205,7 @@ void geCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI *vx, int isV</td>
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205
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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206
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="p">}</span></span>
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207
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">sliceDir</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">GE DTI only tested for axial acquisitions (solution: use Xiangrui Li's dicm2nii)</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">Limited validation for non-Axial DTI: confirm gradient vector transformation.</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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209
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//GE vectors from Xiangrui Li' dicm2nii, validated with datasets from https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging</span></span>
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210
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">ivec3</span> <span class="n" style="color: #333;">flp</span><span class="p">;</span></span>
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211
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">sliceDir</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -292,9 +292,9 @@ void siemensPhilipsCorrectBvecs(struct TDICOMdata *d, int sliceDir, struct TDTI</td>
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292
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//convert DTI vectors from scanner coordinates to image frame of reference</span></span>
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293
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Uses 6 orient values from ImageOrientationPatient (0020,0037)</span></span>
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294
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// requires PatientPosition 0018,5100 is HFS (head first supine)</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_BRUKER</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_TOSHIBA</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_HITACHI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_UIH</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_SIEMENS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_PHILIPS</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">isBVecWorldCoordinates</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_BRUKER</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_TOSHIBA</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_HITACHI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_UIH</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_SIEMENS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_PHILIPS</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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296
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
297
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<td class="new_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_UIH</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_UIH</span><span class="p">)</span> <span class="p">{</span></span>
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298
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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299
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">vx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">vx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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300
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -967,6 +967,8 @@ void rescueProtocolName(struct TDICOMdata *d, const char * filename) {</td>
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<td class="old_line diff-line-num" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
967
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<td class="new_line diff-line-num" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">protocolName</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">],</span> <span class="n" style="color: #333;">fmriExternalInfo</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">],</span> <span class="n" style="color: #333;">coilID</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">],</span> <span class="n" style="color: #333;">consistencyInfo</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">],</span> <span class="n" style="color: #333;">coilElements</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">],</span> <span class="n" style="color: #333;">pulseSequenceDetails</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">],</span> <span class="n" style="color: #333;">wipMemBlock</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStrLarge</span><span class="p">];</span></span>
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968
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<td class="new_line diff-line-num" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="cpp"> <span class="n" style="color: #333;">TCsaAscii</span> <span class="n" style="color: #333;">csaAscii</span><span class="p">;</span></span>
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969
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<td class="new_line diff-line-num" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
969
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="cpp"> <span class="n" style="color: #333;">siemensCsaAscii</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">csaAscii</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">SeriesHeader_offset</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">SeriesHeader_length</span><span class="p">,</span> <span class="n" style="color: #333;">shimSetting</span><span class="p">,</span> <span class="n" style="color: #333;">coilID</span><span class="p">,</span> <span class="n" style="color: #333;">consistencyInfo</span><span class="p">,</span> <span class="n" style="color: #333;">coilElements</span><span class="p">,</span> <span class="n" style="color: #333;">pulseSequenceDetails</span><span class="p">,</span> <span class="n" style="color: #333;">fmriExternalInfo</span><span class="p">,</span> <span class="n" style="color: #333;">protocolName</span><span class="p">,</span> <span class="n" style="color: #333;">wipMemBlock</span><span class="p">);</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">protocolName</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">kDICOMStr</span><span class="p">)</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="n" style="color: #333;">protocolName</span><span class="p">[</span><span class="n" style="color: #333;">kDICOMStr</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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970
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972
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">protocolName</span><span class="p">,</span> <span class="n" style="color: #333;">protocolName</span><span class="p">);</span></span>
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971
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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972
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1139,6 +1141,8 @@ tse3d: T2*/</td>
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1139
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">REAL"</span><span class="p">);</span></span>
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1140
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isHasImaginary</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_GE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imageType</span><span class="p">,</span> <span class="s" style="color: #d14;">"_IMAGINARY_"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span> <span class="p">)</span> </span>
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1141
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">IMAGINARY"</span><span class="p">);</span></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isRealIsPhaseMapHz</span><span class="p">))</span><span class="c1" style="color: #998; font-style: italic;">// && ((d.manufacturer == kMANUFACTURER_GE) || (strstr(d.imageType, "_IMAGINARY_") == NULL)) ) </span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">FIELDMAPHZ"</span><span class="p">);</span></span>
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1142
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1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">],</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> </span>
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1143
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp"> <span class="p">}</span></span>
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1144
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1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//DICOM is derived image or non-spatial file (sounds, etc)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1372,7 +1376,7 @@ tse3d: T2*/</td>
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1372
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1376
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<pre style="margin: 0;"> <span id="LC1376" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } //for k */</span></span>
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1373
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1377
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<pre style="margin: 0;"> <span id="LC1377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//vessel locations</span></span>
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1374
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1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">newstr</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">];</span></span>
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1375
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<pre style="margin: 0;">-<span id="LC1375" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">newstr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">sWipMemBlock<span class="idiff left right">.</span>AdFree%d</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: %%g,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">newstr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">sWipMemBlockAdFree%d</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: %%g,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//issue483: sWipMemBlock.AdFree -> sWipMemBlockAdFree</span></span></span>
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1376
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1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="cpp"> <span class="n" style="color: #333;">json_FloatNotNan</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">newstr</span><span class="p">,</span> <span class="n" style="color: #333;">csaAscii</span><span class="p">.</span><span class="n" style="color: #333;">adFree</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC1381" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1382" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1542,11 +1546,10 @@ tse3d: T2*/</td>
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<pre style="margin: 0;"> <span id="LC1546" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// effectiveEchoSpacing = d.CSA.sliceMeasurementDuration / (reconMatrixPE * 1000.0);</span></span>
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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">reconMatrixPE</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">bandwidthPerPixelPhaseEncode</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="cpp"> <span class="n" style="color: #333;">effectiveEchoSpacing</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">bandwidthPerPixelPhaseEncode</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">reconMatrixPE</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">effectiveEchoSpacingGE</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1546" class="line" lang="cpp"> <span class="n" style="color: #333;">effectiveEchoSpacing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">effectiveEchoSpacingGE</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1000000.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1547" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">effectiveEchoSpacing</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">fieldStrength</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">waterFatShift</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">echoTrainLength</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">reconMatrixPE</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1548" class="line" lang="cpp"> <span class="n" style="color: #333;">json_Float</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">WaterFatShift</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: %g,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">waterFatShift</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1549" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//https://github.com/rordenlab/dcm2niix/issues/377</span></span>
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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="cpp"> <span class="n" style="color: #333;">json_Float</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">WaterFatShift</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: %g,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">waterFatShift</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1550" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">effectiveEchoSpacing</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imagingFrequency</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">waterFatShift</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">echoTrainLength</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">reconMatrixPE</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//in theory we could use either fieldStrength or imagingFrequency, but the former is typically provided with low precision</span></span>
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<pre style="margin: 0;">+<span id="LC1552" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//https://github.com/rordenlab/dcm2niix/issues/377</span></span>
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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// EchoSpacing 1/BW/EPI_factor https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1308&L=FSL&D=0&P=113520</span></span>
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<pre style="margin: 0;"> <span id="LC1554" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this formula from https://support.brainvoyager.com/brainvoyager/functional-analysis-preparation/29-pre-processing/78-epi-distortion-correction-echo-spacing-and-bandwidth</span></span>
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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// https://neurostars.org/t/consolidating-epi-echo-spacing-and-readout-time-for-philips-scanner/4406</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1560,12 +1563,22 @@ tse3d: T2*/</td>
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<pre style="margin: 0;"> <span id="LC1563" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ReconMatrixPE = 0028,0010 or 0028,0011 depending on 0018,1312</span></span>
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<pre style="margin: 0;"> <span id="LC1564" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC1565" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC1563" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">actualEchoSpacing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">waterFatShift</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imagingFrequency</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">3.4</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">echoTrainLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC1566" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">actualEchoSpacing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">waterFatShift</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">imagingFrequency</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">3.4</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">echoTrainLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">totalReadoutTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">actualEchoSpacing</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">echoTrainLength</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1568" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">effectiveEchoSpacingPhil</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">totalReadoutTime</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">reconMatrixPE</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="cpp"> <span class="n" style="color: #333;">json_Float</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">EstimatedEffectiveEchoSpacing</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: %g,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">effectiveEchoSpacingPhil</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1567" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">EstimatedTotalReadoutTime</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: %g,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">totalReadoutTime</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1568" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1570" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">EstimatedTotalReadoutTime</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: %g,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">totalReadoutTime</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">effectiveEchoSpacingGE</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//TotalReadoutTime = [ ceil (PE_AcquisitionMatrix / Asset_R_factor) - 1] * ESP</span></span>
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">roundFactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span><span class="p">;</span></span>
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1576
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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">isPartialFourier</span><span class="p">)</span> <span class="n" style="color: #333;">roundFactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">4.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1577" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">totalReadoutTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">ceil</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">roundFactor</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">phaseEncodingLines</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">accelFactPE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">roundFactor</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">effectiveEchoSpacingGE</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.000001</span><span class="p">;</span></span>
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1578
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<pre style="margin: 0;">+<span id="LC1578" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("ASSET= %g PE_AcquisitionMatrix= %d ESP= %d TotalReadoutTime= %g\n", d.accelFactPE, d.phaseEncodingLines, d.effectiveEchoSpacingGE, totalReadoutTime);</span></span>
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1579
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<pre style="margin: 0;">+<span id="LC1579" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//json_Float(fp, "\t\"TotalReadoutTime\": %g,\n", totalReadoutTime);</span></span>
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1580
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<pre style="margin: 0;">+<span id="LC1580" class="line" lang="cpp"> <span class="n" style="color: #333;">effectiveEchoSpacing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">totalReadoutTime</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">reconMatrixPE</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> </span>
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1581
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<pre style="margin: 0;">+<span id="LC1581" class="line" lang="cpp"> <span class="p">}</span></span>
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1569
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1582
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<pre style="margin: 0;"> <span id="LC1582" class="line" lang="cpp"> <span class="n" style="color: #333;">json_Float</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">EffectiveEchoSpacing</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: %g,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">effectiveEchoSpacing</span><span class="p">);</span></span>
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1570
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1583
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<pre style="margin: 0;"> <span id="LC1583" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Calculate true echo spacing (should match what Siemens reports on the console)</span></span>
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1571
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1584
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<pre style="margin: 0;"> <span id="LC1584" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// i.e., should match "echoSpacing" extracted from the ASCII CSA header, when that exists</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1635,7 +1648,7 @@ tse3d: T2*/</td>
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1635
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1648
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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//only save PhaseEncodingDirection if BOTH direction and POLARITY are known</span></span>
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1636
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1649
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Slice Timing UIH or GE >>>></span></span>
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1637
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1650
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//in theory, we should also report XA10 slice times here, but see series 24 of https://github.com/rordenlab/dcm2niix/issues/236</span></span>
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1638
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<pre style="margin: 0;">-<span id="LC1638" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">modality</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMODALITY_PT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">is3DAcq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="p">{</span></span>
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1651
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<pre style="margin: 0;">+<span id="LC1651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">modality</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;"><span class="idiff left">kMODALITY_CT</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">modality</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">kMODALITY_PT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">is3DAcq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="p">{</span></span>
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1639
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1652
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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">SliceTiming</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">: [</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1640
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1653
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<pre style="margin: 0;"> <span id="LC1653" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1641
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1654
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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1669,6 +1682,7 @@ dti4D->volumeOnsetTime[0] = -1;</td>
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1669
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1682
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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">decayFactor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1670
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1683
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<pre style="margin: 0;"> <span id="LC1683" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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1671
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1684
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<pre style="margin: 0;"> <span id="LC1684" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">repetitionTimeExcitation</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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1685
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<pre style="margin: 0;">+<span id="LC1685" class="line" lang="cpp"><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">repetitionTimeInversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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1672
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1686
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<pre style="margin: 0;"> <span id="LC1686" class="line" lang="cpp"><span class="n" style="color: #333;">nii_SaveBIDSX</span><span class="p">(</span><span class="n" style="color: #333;">pathoutname</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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1673
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1687
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<pre style="margin: 0;"> <span id="LC1687" class="line" lang="cpp"><span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">// nii_SaveBIDSX()</span></span>
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1674
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1688
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<pre style="margin: 0;"> <span id="LC1688" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2011,6 +2025,10 @@ int * nii_saveDTI(char pathoutname[],int nConvert, struct TDCMsort dcmSort[],str</td>
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2011
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2025
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<pre style="margin: 0;"> <span id="LC2025" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numDti</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//warning structure not changed outside scope!</span></span>
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2012
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<td class="new_line diff-line-num" data-linenumber="2026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2026
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<pre style="margin: 0;"> <span id="LC2026" class="line" lang="cpp"> <span class="n" style="color: #333;">geCorrectBvecs</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">],</span><span class="n" style="color: #333;">sliceDir</span><span class="p">,</span> <span class="n" style="color: #333;">vx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isVerbose</span><span class="p">);</span></span>
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2013
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2027
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<pre style="margin: 0;"> <span id="LC2027" class="line" lang="cpp"> <span class="n" style="color: #333;">siemensPhilipsCorrectBvecs</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">],</span><span class="n" style="color: #333;">sliceDir</span><span class="p">,</span> <span class="n" style="color: #333;">vx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isVerbose</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2028
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<pre style="margin: 0;">+<span id="LC2028" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//issue449</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2029
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<pre style="margin: 0;">+<span id="LC2029" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">vx</span><span class="p">);</span></span>
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2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2031
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<pre style="margin: 0;">+<span id="LC2031" class="line" lang="cpp"> <span class="p">}</span></span>
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2014
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2032
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<pre style="margin: 0;"> <span id="LC2032" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isFlipY</span> <span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//!FLIP_Y&& (dcmList[indx0].CSA.mosaicSlices < 2) mosaics are always flipped in the Y direction</span></span>
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2015
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<td class="new_line diff-line-num" data-linenumber="2033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2033
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">numDti</span><span class="p">);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2016
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<td class="new_line diff-line-num" data-linenumber="2034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2034
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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">vx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">V</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FLT_EPSILON</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2302,15 +2320,16 @@ bool intensityScaleVaries(int nConvert, struct TDCMsort dcmSort[],struct TDICOMd</td>
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2302
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2320
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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//some Siemens PET scanners generate 16-bit images where slice has its own scaling factor.</span></span>
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2303
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2321
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<pre style="margin: 0;"> <span id="LC2321" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// since NIfTI provides a single scaling factor for each file, these images require special consideration</span></span>
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2304
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2322
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<pre style="margin: 0;"> <span id="LC2322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2305
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<pre style="margin: 0;">-<span id="LC2305" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">iVaries</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">;</span></span>
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2323
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<pre style="margin: 0;">+<span id="LC2323" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dcmList</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">dcmSort</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">indx</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">bitsAllocated</span></span><span class="p">;</span></span>
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2306
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2324
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<pre style="margin: 0;"> <span id="LC2324" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">iScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScale</span><span class="p">;</span></span>
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2307
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2325
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<pre style="margin: 0;"> <span id="LC2325" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">iInter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenIntercept</span><span class="p">;</span></span>
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2308
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2326
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<pre style="margin: 0;"> <span id="LC2326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nConvert</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//stack additional images</span></span>
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2309
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2327
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<pre style="margin: 0;"> <span id="LC2327" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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2310
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<pre style="margin: 0;">-<span id="LC2310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScale</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">iScale</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FLT_EPSILON</span><span class="p">)</span> <span class="n" style="color: #333;">iVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2311
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<pre style="margin: 0;">-<span id="LC2311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenIntercept</span><span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">iInter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FLT_EPSILON</span><span class="p">)</span> <span class="n" style="color: #333;">iVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2328
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<pre style="margin: 0;">+<span id="LC2328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">bitsAllocated</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">dt</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2329
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<pre style="margin: 0;">+<span id="LC2329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScale</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">iScale</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FLT_EPSILON</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2330
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<pre style="margin: 0;">+<span id="LC2330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenIntercept</span><span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">iInter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FLT_EPSILON</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2312
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2331
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<pre style="margin: 0;"> <span id="LC2331" class="line" lang="cpp"> <span class="p">}</span></span>
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2313
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<pre style="margin: 0;">-<span id="LC2313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">iVaries</span></span><span class="p">;</span></span>
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2332
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<pre style="margin: 0;">+<span id="LC2332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">false</span></span><span class="p">;</span></span>
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2314
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2333
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<pre style="margin: 0;"> <span id="LC2333" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//intensityScaleVaries()</span></span>
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2315
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2334
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<pre style="margin: 0;"> <span id="LC2334" class="line" lang="cpp"></span>
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2316
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2335
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<pre style="margin: 0;"> <span id="LC2335" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*unsigned char * nii_bgr2rgb(unsigned char* bImg, struct nifti_1_header *hdr) {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2649,8 +2668,8 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt</td>
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2649
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2668
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<pre style="margin: 0;"> <span id="LC2668" class="line" lang="cpp"> <span class="n" style="color: #333;">strcat</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span><span class="n" style="color: #333;">newstr</span><span class="p">);</span></span>
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2650
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<td class="new_line diff-line-num" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2669
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<pre style="margin: 0;"> <span id="LC2669" class="line" lang="cpp"> <span class="n" style="color: #333;">isEchoReported</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2651
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<td class="new_line diff-line-num" data-linenumber="2670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2670
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<pre style="margin: 0;"> <span id="LC2670" class="line" lang="cpp"> <span class="p">}</span></span>
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2652
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<td class="new_line diff-line-num old" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2652" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isImageNumReported</span><span class="p">))</span> <span class="p">{</span></span>
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2653
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<td class="new_line diff-line-num old" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2653" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">newstr</span><span class="p">,</span> <span class="s" style="color: #d14;">"_i%05d"</span><span class="p">,</span> <span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2671
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<pre style="margin: 0;">+<span id="LC2671" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isImageNumReported</span><span class="p">))</span> <span class="p">{</span></span>
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2672
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<pre style="margin: 0;">+<span id="LC2672" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">newstr</span><span class="p">,</span> <span class="s" style="color: #d14;">"_i%05d"</span><span class="p">,</span> <span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span><span class="p">);</span></span>
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2654
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2673
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<pre style="margin: 0;"> <span id="LC2673" class="line" lang="cpp"> <span class="n" style="color: #333;">strcat</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span><span class="n" style="color: #333;">newstr</span><span class="p">);</span></span>
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2655
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2674
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<pre style="margin: 0;"> <span id="LC2674" class="line" lang="cpp"> <span class="p">}</span></span>
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2656
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2675
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<pre style="margin: 0;"> <span id="LC2675" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (dcm.maxGradDynVol > 0) { //Philips segmented</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2660,7 +2679,10 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt</td>
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2660
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2679
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<pre style="margin: 0;"> <span id="LC2679" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isAddNamePostFixes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isHasImaginary</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2661
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<td class="new_line diff-line-num" data-linenumber="2680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2680
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<pre style="margin: 0;"> <span id="LC2680" class="line" lang="cpp"> <span class="n" style="color: #333;">strcat</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span><span class="s" style="color: #d14;">"_imaginary"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//has phase map</span></span>
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<td class="old_line diff-line-num" data-linenumber="2662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2662
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<td class="new_line diff-line-num" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2681
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<pre style="margin: 0;"> <span id="LC2681" class="line" lang="cpp"> <span class="p">}</span></span>
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2663
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<td class="new_line diff-line-num old" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2663" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isAddNamePostFixes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isHasReal</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2682
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<pre style="margin: 0;">+<span id="LC2682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isAddNamePostFixes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isHasReal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isRealIsPhaseMapHz</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2683
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<pre style="margin: 0;">+<span id="LC2683" class="line" lang="cpp"> <span class="n" style="color: #333;">strcat</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span><span class="s" style="color: #d14;">"_fieldmaphz"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//has field map</span></span>
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2684
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<pre style="margin: 0;">+<span id="LC2684" class="line" lang="cpp"> <span class="p">}</span></span>
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2685
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<pre style="margin: 0;">+<span id="LC2685" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isAddNamePostFixes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isHasReal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isRealIsPhaseMapHz</span><span class="p">))</span> <span class="p">{</span></span>
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2664
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2686
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<pre style="margin: 0;"> <span id="LC2686" class="line" lang="cpp"> <span class="n" style="color: #333;">strcat</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span><span class="s" style="color: #d14;">"_real"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//has phase map</span></span>
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2665
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2687
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<pre style="margin: 0;"> <span id="LC2687" class="line" lang="cpp"> <span class="p">}</span></span>
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2666
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2688
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<pre style="margin: 0;"> <span id="LC2688" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isAddNamePostFixes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcm</span><span class="p">.</span><span class="n" style="color: #333;">isHasPhase</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2690,7 +2712,7 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt</td>
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2690
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2712
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<pre style="margin: 0;"> <span id="LC2712" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2691
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<td class="new_line diff-line-num" data-linenumber="2713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2713
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<pre style="margin: 0;"> <span id="LC2713" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(_WIN64) || defined(_WIN32) || defined(kMASK_WINDOWS_SPECIAL_CHARACTERS)//https://stackoverflow.com/questions/1976007/what-characters-are-forbidden-in-windows-and-linux-directory-names</span></span>
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<td class="old_line diff-line-num" data-linenumber="2692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2692
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2714
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<pre style="margin: 0;"> <span id="LC2714" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">);</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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2693
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<pre style="margin: 0;">-<span id="LC2693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\\'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'/'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'<'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">':'</span><span class="p">)</span></span>
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2715
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<pre style="margin: 0;">+<span id="LC2715" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\\'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'/'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'<'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">':'</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outname</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">';'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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2694
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2716
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<pre style="margin: 0;"> <span id="LC2716" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'"'</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// || (outname[pos] == '/') || (outname[pos] == '\\')</span></span>
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2695
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2717
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<pre style="margin: 0;"> <span id="LC2717" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//|| (outname[pos] == '^') issue398</span></span>
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2696
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2718
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<pre style="margin: 0;"> <span id="LC2718" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'*'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'|'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2714,6 +2736,18 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt</td>
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2714
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2736
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<pre style="margin: 0;"> <span id="LC2736" class="line" lang="cpp"> <span class="n" style="color: #333;">appendChar</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPathSeparator</span><span class="p">;</span></span>
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2715
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2737
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<pre style="margin: 0;"> <span id="LC2737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">pth</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pth</span><span class="p">[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">pth</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kPathSeparator</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kPathSeparator</span><span class="p">))</span></span>
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2716
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2738
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<pre style="margin: 0;"> <span id="LC2738" class="line" lang="cpp"> <span class="n" style="color: #333;">strcat</span> <span class="p">(</span><span class="n" style="color: #333;">baseoutname</span><span class="p">,</span><span class="n" style="color: #333;">appendChar</span><span class="p">);</span></span>
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2739
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<pre style="margin: 0;">+<span id="LC2739" class="line" lang="cpp"> </span>
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2740
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<pre style="margin: 0;">+<span id="LC2740" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//remove redundant underscores</span></span>
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2741
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<pre style="margin: 0;">+<span id="LC2741" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">);</span></span>
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2742
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<pre style="margin: 0;">+<span id="LC2742" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2743
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<pre style="margin: 0;">+<span id="LC2743" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">inpos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="n" style="color: #333;">inpos</span> <span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2744
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<pre style="margin: 0;">+<span id="LC2744" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">outpos</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">inpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">outpos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">))</span></span>
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2745
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<pre style="margin: 0;">+<span id="LC2745" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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2746
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<pre style="margin: 0;">+<span id="LC2746" class="line" lang="cpp"> <span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">outpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">inpos</span><span class="p">];</span></span>
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2747
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<pre style="margin: 0;">+<span id="LC2747" class="line" lang="cpp"> <span class="n" style="color: #333;">outpos</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2748
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<pre style="margin: 0;">+<span id="LC2748" class="line" lang="cpp"> <span class="p">}</span></span>
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2749
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<pre style="margin: 0;">+<span id="LC2749" class="line" lang="cpp"> <span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">outpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2750
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<pre style="margin: 0;">+<span id="LC2750" class="line" lang="cpp"> </span>
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2717
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2751
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<pre style="margin: 0;"> <span id="LC2751" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Allow user to specify new folders, e.g. "-f dir/%p" or "-f %s/%p/%m"</span></span>
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2718
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2752
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<pre style="margin: 0;"> <span id="LC2752" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// These folders are created if they do not exist</span></span>
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2719
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2753
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<pre style="margin: 0;"> <span id="LC2753" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">kPathSeparator</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2741,16 +2775,6 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt</td>
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2741
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2775
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<pre style="margin: 0;"> <span id="LC2775" class="line" lang="cpp"> <span class="n" style="color: #333;">strcat</span> <span class="p">(</span><span class="n" style="color: #333;">newdir</span><span class="p">,</span><span class="n" style="color: #333;">ch</span><span class="p">);</span></span>
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2742
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2776
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<pre style="margin: 0;"> <span id="LC2776" class="line" lang="cpp"> <span class="p">}</span></span>
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2743
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2777
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<pre style="margin: 0;"> <span id="LC2777" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2744" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//remove redundant underscores</span></span>
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<pre style="margin: 0;">-<span id="LC2745" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2746" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2747" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">inpos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="n" style="color: #333;">inpos</span> <span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2748
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<pre style="margin: 0;">-<span id="LC2748" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">outpos</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">inpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">outpos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'_'</span><span class="p">))</span></span>
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2749
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<pre style="margin: 0;">-<span id="LC2749" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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2750
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<pre style="margin: 0;">-<span id="LC2750" class="line" lang="cpp"> <span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">outpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">inpos</span><span class="p">];</span></span>
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2751
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<pre style="margin: 0;">-<span id="LC2751" class="line" lang="cpp"> <span class="n" style="color: #333;">outpos</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> </span>
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2752
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<pre style="margin: 0;">-<span id="LC2752" class="line" lang="cpp"> <span class="p">}</span></span>
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2753
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<pre style="margin: 0;">-<span id="LC2753" class="line" lang="cpp"> <span class="n" style="color: #333;">outname</span><span class="p">[</span><span class="n" style="color: #333;">outpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2778" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("path='%s' name='%s'\n", pathoutname, outname);</span></span>
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<pre style="margin: 0;"> <span id="LC2779" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//make sure outname is unique</span></span>
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<pre style="margin: 0;"> <span id="LC2780" class="line" lang="cpp"> <span class="n" style="color: #333;">strcat</span> <span class="p">(</span><span class="n" style="color: #333;">baseoutname</span><span class="p">,</span><span class="n" style="color: #333;">outname</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3453,8 +3477,10 @@ void swapEndian(struct nifti_1_header* hdr, unsigned char* im, bool isNative) {</td>
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3477
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<pre style="margin: 0;"> <span id="LC3477" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nii_saveNII</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">niiFilename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">nifti_1_header</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMopts</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC3478" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isOnlyBIDS</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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3479
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<pre style="margin: 0;"> <span id="LC3479" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isSaveNRRD</span><span class="p">)</span> <span class="p">{</span></span>
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3456
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<pre style="margin: 0;">-<span id="LC3456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="n" style="color: #333;">dti4D</span><span class="p">;</span></span>
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3457
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<pre style="margin: 0;">-<span id="LC3457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nii_saveNRRD</span><span class="p">(</span><span class="n" style="color: #333;">niiFilename</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dti4D</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3480
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<pre style="margin: 0;">+<span id="LC3480" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dti4D</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3481
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<pre style="margin: 0;">+<span id="LC3481" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nii_saveNRRD</span><span class="p">(</span><span class="n" style="color: #333;">niiFilename</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3482
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<pre style="margin: 0;">+<span id="LC3482" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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3483
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<pre style="margin: 0;">+<span id="LC3483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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3458
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3484
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<pre style="margin: 0;"> <span id="LC3484" class="line" lang="cpp"> <span class="p">}</span></span>
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3459
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3485
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<pre style="margin: 0;"> <span id="LC3485" class="line" lang="cpp"> <span class="n" style="color: #333;">hdr</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">352</span><span class="p">;</span></span>
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3460
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3486
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<pre style="margin: 0;"> <span id="LC3486" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">imgsz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nii_ImgBytes</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4282,7 +4308,8 @@ float PhilipsPreciseVal (float lPV, float lRS, float lRI, float lSS) {</td>
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4282
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4308
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<pre style="margin: 0;"> <span id="LC4308" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PhilipsPrecise</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isPhilipsFloatNotDisplayScaling</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">nifti_1_header</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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4283
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4309
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<pre style="margin: 0;"> <span id="LC4309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMANUFACTURER_PHILIPS</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//not Philips</span></span>
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4284
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<td class="new_line diff-line-num" data-linenumber="4310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4310
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<pre style="margin: 0;"> <span id="LC4310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isScaleVariesEnh</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//issue363 rescaled before slice reordering</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4285
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<pre style="margin: 0;">-<span id="LC4285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">RWVScale</span><span class="p">))</span> <span class="p">{</span></span>
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4311
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<pre style="margin: 0;">+<span id="LC4311" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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4312
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<pre style="margin: 0;">+<span id="LC4312" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (!isSameFloatGE(0.0, d->RWVScale)) { //https://github.com/rordenlab/dcm2niix/issues/493</span></span>
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4286
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4313
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<pre style="margin: 0;"> <span id="LC4313" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> h->scl_slope = d->RWVScale;</span></span>
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4287
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<td class="new_line diff-line-num" data-linenumber="4314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4314
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<pre style="margin: 0;"> <span id="LC4314" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> h->scl_inter = d->RWVIntercept;</span></span>
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4288
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4315
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<pre style="margin: 0;"> <span id="LC4315" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printMessage("Using RWVSlope:RWVIntercept = %g:%g\n",d->RWVScale,d->RWVIntercept);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4293,7 +4320,7 @@ void PhilipsPrecise(struct TDICOMdata * d, bool isPhilipsFloatNotDisplayScaling,</td>
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4293
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4320
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<pre style="margin: 0;"> <span id="LC4320" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printMessage(" RS = rescale slope, RI = rescale intercept, SS = scale slope\n");</span></span>
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4294
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4321
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<pre style="margin: 0;"> <span id="LC4321" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printMessage(" D = R * RS + RI , P = D/(RS * SS)\n");</span></span>
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4295
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4322
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<pre style="margin: 0;"> <span id="LC4322" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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4296
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<pre style="margin: 0;">-<span id="LC4296" class="line" lang="cpp"> <span class="p">}</span></span>
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4323
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<pre style="margin: 0;">+<span id="LC4323" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }<span class="idiff left right">*/</span></span></span>
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4297
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4324
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<pre style="margin: 0;"> <span id="LC4324" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScalePhilips</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//no Philips Precise</span></span>
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4298
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4325
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<pre style="margin: 0;"> <span id="LC4325" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//we will report calibrated "FP" values http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998685/</span></span>
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4299
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4326
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<pre style="margin: 0;"> <span id="LC4326" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">l0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PhilipsPreciseVal</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScale</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenIntercept</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4451,6 +4478,8 @@ void checkSliceTiming(struct TDICOMdata * d, struct TDICOMdata * d1, int verbose</td>
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4451
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4478
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<pre style="margin: 0;"> <span id="LC4478" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">nSlices</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kMaxEPI3D</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="n" style="color: #333;">nSlices</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span></span>
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4452
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4479
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<pre style="margin: 0;"> <span id="LC4479" class="line" lang="cpp"> <span class="n" style="color: #333;">nSlices</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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4453
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4480
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<pre style="margin: 0;"> <span id="LC4480" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nSlices</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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4481
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<pre style="margin: 0;">+<span id="LC4481" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="n" style="color: #333;">kMaxEPI3D</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>
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4482
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<pre style="margin: 0;">+<span id="LC4482" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Adjusting for negative MosaicRefAcqTimes (issue 271).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> </span>
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4454
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4483
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<pre style="margin: 0;"> <span id="LC4483" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isSliceTimeHHMMSS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMANUFACTURER_UIH</span><span class="p">);</span></span>
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4455
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4484
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<pre style="margin: 0;"> <span id="LC4484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isForceSliceTimeHHMMSS</span><span class="p">)</span> <span class="n" style="color: #333;">isSliceTimeHHMMSS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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4456
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4485
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<pre style="margin: 0;"> <span id="LC4485" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (d->isXA10A) isSliceTimeHHMMSS = true; //for XA10 use TimeAfterStart 0x0021,0x1104 -> Siemens de-identification can corrupt acquisition ties https://github.com/rordenlab/dcm2niix/issues/236</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4989,8 +5018,9 @@ int sliceTimingCore(struct TDCMsort *dcmSort,struct TDICOMdata *dcmList, struct</td>
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4989
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5018
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<pre style="margin: 0;"> <span id="LC5018" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//uint64_t indx0 = dcmSort[0].indx;</span></span>
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4990
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5019
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<pre style="margin: 0;"> <span id="LC5019" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//uint64_t indx1 = dcmSort[1].indx;</span></span>
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4991
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5020
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<pre style="margin: 0;"> <span id="LC5020" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">];</span></span>
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4992
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<pre style="margin: 0;">-<span id="LC4992" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indx1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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4993
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<pre style="margin: 0;">-<span id="LC4993" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">indx1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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5021
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<pre style="margin: 0;">+<span id="LC5021" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indx1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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5022
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<pre style="margin: 0;">+<span id="LC5022" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//use 2nd volume as CMRR bug can create bogus slice timing in first volume</span></span>
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5023
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<pre style="margin: 0;">+<span id="LC5023" class="line" lang="cpp"> <span class="n" style="color: #333;">indx1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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4994
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5024
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<pre style="margin: 0;"> <span id="LC5024" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx1</span><span class="p">];</span></span>
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4995
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5025
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<pre style="margin: 0;"> <span id="LC5025" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//oldSliceTimingGE(dcmSort, dcmList, hdr, verbose, filename, nConvert);</span></span>
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4996
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5026
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<pre style="margin: 0;"> <span id="LC5026" class="line" lang="cpp"> <span class="n" style="color: #333;">sliceTimingUIH</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">nConvert</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5011,7 +5041,12 @@ int sliceTimingCore(struct TDCMsort *dcmSort,struct TDICOMdata *dcmList, struct</td>
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5011
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5041
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<pre style="margin: 0;"> <span id="LC5041" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">protocolSliceNumber1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5012
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5042
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<pre style="margin: 0;"> <span id="LC5042" class="line" lang="cpp"> <span class="p">}</span></span>
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5013
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5043
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<pre style="margin: 0;"> <span id="LC5043" class="line" lang="cpp"> <span class="n" style="color: #333;">sliceTimingGE</span><span class="p">(</span><span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">);</span></span>
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5044
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<pre style="margin: 0;">+<span id="LC5044" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//ensure slice times have variability</span></span>
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5014
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5045
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<pre style="margin: 0;"> <span id="LC5045" class="line" lang="cpp"> <span class="n" style="color: #333;">reverseSliceTiming</span><span class="p">(</span><span class="n" style="color: #333;">d0</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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5046
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<pre style="margin: 0;">+<span id="LC5046" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">allSame</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5047
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<pre style="margin: 0;">+<span id="LC5047" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="5048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5048
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<pre style="margin: 0;">+<span id="LC5048" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">d0</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">d0</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="n" style="color: #333;">allSame</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5049
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<pre style="margin: 0;">+<span id="LC5049" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allSame</span><span class="p">)</span> <span class="n" style="color: #333;">d0</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">sliceTiming</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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5015
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5050
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<pre style="margin: 0;"> <span id="LC5050" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sliceDir</span><span class="p">;</span></span>
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5016
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5051
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<pre style="margin: 0;"> <span id="LC5051" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//sliceTiming()</span></span>
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5017
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5052
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<pre style="margin: 0;"> <span id="LC5052" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5080,12 +5115,14 @@ void loadOverlay(char* imgname, unsigned char * img, int offset, int x, int y, i</td>
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5080
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5115
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<pre style="margin: 0;"> <span id="LC5115" class="line" lang="cpp"></span>
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5081
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5116
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<pre style="margin: 0;"> <span id="LC5116" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">saveDcm2NiiCore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMsort</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[],</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[],</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TSearchList</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMopts</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dti4D</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">segVol</span><span class="p">)</span> <span class="p">{</span></span>
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5082
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<td class="new_line diff-line-num" data-linenumber="5117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5117
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<pre style="margin: 0;"> <span id="LC5117" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">iVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intensityScaleVaries</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span><span class="n" style="color: #333;">dcmSort</span><span class="p">,</span><span class="n" style="color: #333;">dcmList</span><span class="p">);</span></span>
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5083
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<td class="new_line diff-line-num old" data-linenumber="5118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5083" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sliceMMarray</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//only used if slices are not equidistant</span></span>
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5118
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<pre style="margin: 0;">+<span id="LC5118" class="line" lang="cpp"><span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sliceMMarray</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//only used if slices are not equidistant</span></span>
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5084
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5119
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<pre style="margin: 0;"> <span id="LC5119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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5085
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5120
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<pre style="margin: 0;"> <span id="LC5120" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indx0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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5086
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5121
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<pre style="margin: 0;"> <span id="LC5121" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indx1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indx0</span><span class="p">;</span></span>
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5087
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5122
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<pre style="margin: 0;"> <span id="LC5122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">indx1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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5088
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5123
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<pre style="margin: 0;"> <span id="LC5123" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indxEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="n" style="color: #333;">nConvert</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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5124
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<pre style="margin: 0;">+<span id="LC5124" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">repetitionTimeInversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//only set for Siemens and GE 3D T1 "TR"</span></span>
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5125
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<pre style="margin: 0;">+<span id="LC5125" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">repetitionTimeExcitation</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//only set for Philips 3D T1 "TR"</span></span>
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5089
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5126
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<pre style="margin: 0;"> <span id="LC5126" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef newTilt //see issue 254</span></span>
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5090
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5127
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<pre style="margin: 0;"> <span id="LC5127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span> <span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">modality</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMODALITY_CT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">isXRay</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">gantryTilt</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//issue372: enhanced DICOMs can also have gantry tilt</span></span>
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5091
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5128
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<pre style="margin: 0;"> <span id="LC5128" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">gantryTilt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">computeGantryTiltPrecise</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">],</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indxEnd</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isVerbose</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5173,8 +5210,13 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc</td>
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5173
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5210
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<pre style="margin: 0;"> <span id="LC5210" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">locationsInAcquisition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">locationsInAcquisitionConflict</span><span class="p">;</span></span>
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5174
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5211
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<pre style="margin: 0;"> <span id="LC5211" class="line" lang="cpp"> <span class="p">}</span> </span>
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5175
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5212
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<pre style="margin: 0;"> <span id="LC5212" class="line" lang="cpp"> <span class="p">}</span></span>
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5176
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<td class="new_line diff-line-num old" data-linenumber="5213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">nAcq</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">locationsInAcquisition</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="n" style="color: #333;">nAcq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nConvert</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">locationsInAcquisition</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5177
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<td class="new_line diff-line-num old" data-linenumber="5213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nAcq</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="5178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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5213
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<pre style="margin: 0;">+<span id="LC5213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">nAcq</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">locationsInAcquisition</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">){</span></span>
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5214
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<pre style="margin: 0;">+<span id="LC5214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">locationsInAcquisition</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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5215
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<pre style="margin: 0;">+<span id="LC5215" class="line" lang="cpp"> <span class="n" style="color: #333;">nAcq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">locationsInAcquisition</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5216
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<pre style="margin: 0;">+<span id="LC5216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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5217
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<pre style="margin: 0;">+<span id="LC5217" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"DICOM images may be missing, expected %d spatial locations per volume, but found %d slices.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">locationsInAcquisition</span><span class="p">,</span> <span class="n" style="color: #333;">nConvert</span><span class="p">);</span></span>
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5218
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<pre style="margin: 0;">+<span id="LC5218" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5219
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<pre style="margin: 0;">+<span id="LC5219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nAcq</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="p">)</span> <span class="p">{</span></span>
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5178
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5220
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<pre style="margin: 0;"> <span id="LC5220" class="line" lang="cpp"> <span class="n" style="color: #333;">nAcq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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5179
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5221
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<pre style="margin: 0;"> <span id="LC5221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nConvert</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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5180
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5222
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<pre style="margin: 0;"> <span id="LC5222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSamePosition</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">]))</span> <span class="n" style="color: #333;">nAcq</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5487,9 +5529,11 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc</td>
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5487
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5529
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<pre style="margin: 0;"> <span id="LC5529" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"|%d|%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">nameList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">]);</span> </span>
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5488
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5530
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<pre style="margin: 0;"> <span id="LC5530" class="line" lang="cpp"> <span class="p">}</span></span>
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5489
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5531
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<pre style="margin: 0;"> <span id="LC5531" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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5532
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<pre style="margin: 0;">+<span id="LC5532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">protocolName</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//beware: tProtocolName can vary within a series "t1+AF8-mpr+AF8-ns+AF8-sag+AF8-p2+AF8-iso" vs "T1_mprage_ns_sag_p2_iso 1.0mm_192"</span></span>
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5533
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<pre style="margin: 0;">+<span id="LC5533" class="line" lang="cpp"> <span class="n" style="color: #333;">rescueProtocolName</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">nameList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">]);</span></span>
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5490
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5534
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<pre style="margin: 0;"> <span id="LC5534" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//move before headerDcm2Nii2 checkSliceTiming(&dcmList[indx0], &dcmList[indx1]);</span></span>
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5491
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5535
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<pre style="margin: 0;"> <span id="LC5535" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">pathoutname</span><span class="p">[</span><span class="mi" style="color: #099;">2048</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">""</span><span class="p">};</span></span>
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5492
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<pre style="margin: 0;">-<span id="LC5492" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nii_createFilename</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">pathoutname</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">)</span> <span class="p">{</span></span>
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5536
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<pre style="margin: 0;">+<span id="LC5536" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nii_createFilename</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">pathoutname</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">)</span> <span class="p">{</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//make sure call is subsequent to rescueProtocolName()</span></span></span>
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5493
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5537
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<pre style="margin: 0;"> <span id="LC5537" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">imgM</span><span class="p">);</span></span>
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5494
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5538
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<pre style="margin: 0;"> <span id="LC5538" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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5495
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5539
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<pre style="margin: 0;"> <span id="LC5539" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5497,8 +5541,24 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc</td>
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5497
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5541
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<pre style="margin: 0;"> <span id="LC5541" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">imgM</span><span class="p">);</span></span>
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5498
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5542
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<pre style="margin: 0;"> <span id="LC5542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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5499
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5543
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<pre style="margin: 0;"> <span id="LC5543" class="line" lang="cpp"> <span class="p">}</span></span>
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5500
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<pre style="margin: 0;">-<span id="LC5500" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//issue377(dcmList[indx0], &hdr0); return EXIT_SUCCESS;</span></span>
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5501
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<pre style="margin: 0;">-<span id="LC5501" class="line" lang="cpp"> <span class="n" style="color: #333;">nii_SaveBIDSX</span><span class="p">(</span><span class="n" style="color: #333;">pathoutname</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hdr0</span><span class="p">,</span> <span class="n" style="color: #333;">nameList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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5544
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<pre style="margin: 0;">+<span id="LC5544" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// skip converting if user has specified one or more series, but has not specified this one</span></span>
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<pre style="margin: 0;">+<span id="LC5545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">numSeries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//issue453: moved to before saveBIDS</span></span>
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5546
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<pre style="margin: 0;">+<span id="LC5546" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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5547
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<pre style="margin: 0;">+<span id="LC5547" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">seriesUidCrc</span><span class="p">;</span></span>
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5548
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<pre style="margin: 0;">+<span id="LC5548" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">segVol</span><span class="p">;</span></span>
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5549
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<pre style="margin: 0;">+<span id="LC5549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">echoNum</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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5550
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<pre style="margin: 0;">+<span id="LC5550" class="line" lang="cpp"> <span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">echoNum</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5551
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<pre style="margin: 0;">+<span id="LC5551" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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5552
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<pre style="margin: 0;">+<span id="LC5552" class="line" lang="cpp"> <span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">10.0</span><span class="p">;</span></span>
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5553
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<pre style="margin: 0;">+<span id="LC5553" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">numSeries</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5554
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<pre style="margin: 0;">+<span id="LC5554" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSameDouble</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">seriesNumber</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">seriesNum</span><span class="p">))</span></span>
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5555
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<pre style="margin: 0;">+<span id="LC5555" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5556
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<pre style="margin: 0;">+<span id="LC5556" class="line" lang="cpp"> <span class="p">}</span></span>
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5557
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<pre style="margin: 0;">+<span id="LC5557" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">numSeries</span><span class="p">)</span></span>
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5558
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<pre style="margin: 0;">+<span id="LC5558" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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5559
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<pre style="margin: 0;">+<span id="LC5559" class="line" lang="cpp"> <span class="p">}</span> </span>
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5560
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<pre style="margin: 0;">+<span id="LC5560" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">numSeries</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//issue453</span></span>
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5561
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<pre style="margin: 0;">+<span id="LC5561" class="line" lang="cpp"> <span class="n" style="color: #333;">nii_SaveBIDSX</span><span class="p">(</span><span class="n" style="color: #333;">pathoutname</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hdr0</span><span class="p">,</span> <span class="n" style="color: #333;">nameList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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5502
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5562
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<pre style="margin: 0;"> <span id="LC5562" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isOnlyBIDS</span><span class="p">)</span> <span class="p">{</span></span>
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5503
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5563
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<pre style="margin: 0;"> <span id="LC5563" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//note we waste time loading every image, however this ensures hdr0 matches actual output</span></span>
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5504
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5564
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<pre style="margin: 0;"> <span id="LC5564" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">imgM</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5535,8 +5595,6 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc</td>
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5535
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5595
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<pre style="margin: 0;"> <span id="LC5595" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">img4D</span><span class="p">);</span></span>
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5536
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5596
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<pre style="margin: 0;"> <span id="LC5596" class="line" lang="cpp"> <span class="n" style="color: #333;">saveAs3D</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5537
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5597
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<pre style="margin: 0;"> <span id="LC5597" class="line" lang="cpp"> <span class="p">}</span></span>
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5538
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<td class="new_line diff-line-num old" data-linenumber="5598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5538" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">protocolName</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//beware: tProtocolName can vary within a series "t1+AF8-mpr+AF8-ns+AF8-sag+AF8-p2+AF8-iso" vs "T1_mprage_ns_sag_p2_iso 1.0mm_192"</span></span>
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5539
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<pre style="margin: 0;">-<span id="LC5539" class="line" lang="cpp"> <span class="n" style="color: #333;">rescueProtocolName</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">nameList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">]);</span></span>
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5540
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5598
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<pre style="margin: 0;"> <span id="LC5598" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Prevent these DICOM files from being reused.</span></span>
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5541
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5599
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<pre style="margin: 0;"> <span id="LC5599" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nConvert</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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5542
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5600
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<pre style="margin: 0;"> <span id="LC5600" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">converted2NII</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5560,26 +5618,6 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc</td>
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5560
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5618
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<pre style="margin: 0;"> <span id="LC5618" class="line" lang="cpp"> <span class="n" style="color: #333;">isFlipZ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5561
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5619
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<pre style="margin: 0;"> <span id="LC5619" class="line" lang="cpp"> <span class="n" style="color: #333;">imgM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nii_flipZ</span><span class="p">(</span><span class="n" style="color: #333;">imgM</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hdr0</span><span class="p">);</span></span>
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5562
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5620
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<pre style="margin: 0;"> <span id="LC5620" class="line" lang="cpp"> <span class="n" style="color: #333;">sliceDir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">sliceDir</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//change this, we have flipped the image so GE DTI bvecs no longer need to be flipped!</span></span>
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5563
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<pre style="margin: 0;">-<span id="LC5563" class="line" lang="cpp"> <span class="p">}</span></span>
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5564
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<pre style="margin: 0;">-<span id="LC5564" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// skip converting if user has specified one or more series, but has not specified this one</span></span>
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5565
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<pre style="margin: 0;">-<span id="LC5565" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">numSeries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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5566
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<pre style="margin: 0;">-<span id="LC5566" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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5567
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<pre style="margin: 0;">-<span id="LC5567" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//double seriesNum = (double) dcmList[dcmSort[0].indx].seriesNum;</span></span>
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5568
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<pre style="margin: 0;">-<span id="LC5568" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">seriesUidCrc</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC5569" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">segVol</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC5570" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">echoNum</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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5571
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<pre style="margin: 0;">-<span id="LC5571" class="line" lang="cpp"> <span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">echoNum</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5572
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<pre style="margin: 0;">-<span id="LC5572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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5573
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<pre style="margin: 0;">-<span id="LC5573" class="line" lang="cpp"> <span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">segVolEcho</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">10.0</span><span class="p">;</span></span>
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5574
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<pre style="margin: 0;">-<span id="LC5574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">numSeries</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5575
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<pre style="margin: 0;">-<span id="LC5575" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSameDouble</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">seriesNumber</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">seriesNum</span><span class="p">))</span> <span class="p">{</span> </span>
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5576
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<pre style="margin: 0;">-<span id="LC5576" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (opts.seriesNumber[i] == dcmList[dcmSort[0].indx].seriesNum) {</span></span>
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5577
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<pre style="margin: 0;">-<span id="LC5577" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5578
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<pre style="margin: 0;">-<span id="LC5578" class="line" lang="cpp"> <span class="p">}</span></span>
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5579
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<pre style="margin: 0;">-<span id="LC5579" class="line" lang="cpp"> <span class="p">}</span></span>
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5580
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<pre style="margin: 0;">-<span id="LC5580" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">numSeries</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC5581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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5582
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<pre style="margin: 0;">-<span id="LC5582" class="line" lang="cpp"> <span class="p">}</span></span>
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5583
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5621
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<pre style="margin: 0;"> <span id="LC5621" class="line" lang="cpp"> <span class="p">}</span></span>
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5584
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5622
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<pre style="margin: 0;"> <span id="LC5622" class="line" lang="cpp"> <span class="n" style="color: #333;">nii_saveText</span><span class="p">(</span><span class="n" style="color: #333;">pathoutname</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hdr0</span><span class="p">,</span> <span class="n" style="color: #333;">nameList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">]);</span></span>
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5585
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5623
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<pre style="margin: 0;"> <span id="LC5623" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numADC</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5722,6 +5760,8 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dc</td>
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5722
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5760
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<pre style="margin: 0;"> <span id="LC5760" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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5723
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5761
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<pre style="margin: 0;"> <span id="LC5761" class="line" lang="cpp"> <span class="n" style="color: #333;">imgM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeADC</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hdr0</span><span class="p">,</span> <span class="n" style="color: #333;">imgM</span><span class="p">,</span> <span class="n" style="color: #333;">numADC</span><span class="p">);</span></span>
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5724
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5762
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<pre style="margin: 0;"> <span id="LC5762" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef USING_R</span></span>
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5763
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<pre style="margin: 0;">+<span id="LC5763" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iVaries</span><span class="p">)</span></span>
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5764
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<pre style="margin: 0;">+<span id="LC5764" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Saving as 32-bit float (slope, intercept or bits allocated varies).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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5725
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5765
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<pre style="margin: 0;"> <span id="LC5765" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isSaveNRRD</span><span class="p">)</span></span>
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5726
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5766
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<pre style="margin: 0;"> <span id="LC5766" class="line" lang="cpp"> <span class="n" style="color: #333;">returnCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nii_saveNRRD</span><span class="p">(</span><span class="n" style="color: #333;">pathoutname</span><span class="p">,</span> <span class="n" style="color: #333;">hdr0</span><span class="p">,</span> <span class="n" style="color: #333;">imgM</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">],</span> <span class="n" style="color: #333;">dti4D</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx0</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span><span class="p">);</span></span>
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5727
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5767
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<pre style="margin: 0;"> <span id="LC5767" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isSave3D</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5807,8 +5847,7 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis</td>
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5807
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5847
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<pre style="margin: 0;"> <span id="LC5847" class="line" lang="cpp"> <span class="p">}</span></span>
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5808
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5848
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<pre style="margin: 0;"> <span id="LC5848" class="line" lang="cpp"> <span class="p">}</span></span>
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5809
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5849
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<pre style="margin: 0;"> <span id="LC5849" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//bvec/bval saved for each series (real, phase, magnitude, imaginary) https://github.com/rordenlab/dcm2niix/issues/219</span></span>
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5810
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<pre style="margin: 0;">-<span id="LC5810" class="line" lang="cpp"> <span class="n" style="color: #333;">TDTI4D</span> <span class="n" style="color: #333;">dti4Ds</span><span class="p">;</span></span>
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5811
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<pre style="margin: 0;">-<span id="LC5811" class="line" lang="cpp"> <span class="n" style="color: #333;">dti4Ds</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dti4D</span><span class="p">;</span></span>
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5850
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<pre style="margin: 0;">+<span id="LC5850" class="line" lang="cpp"> <span class="n" style="color: #333;">TDTI4D</span> <span class="n" style="color: #333;">dti4Ds</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dti4D</span><span class="p">;</span></span>
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5812
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5851
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<pre style="margin: 0;"> <span id="LC5851" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isHasDti</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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5813
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5852
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<pre style="margin: 0;"> <span id="LC5852" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isHasDti</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]))</span> <span class="p">{</span></span>
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5814
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5853
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<pre style="margin: 0;"> <span id="LC5853" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nDti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5825,7 +5864,18 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis</td>
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5825
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5864
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<pre style="margin: 0;"> <span id="LC5864" class="line" lang="cpp"> <span class="p">}</span></span>
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5826
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5865
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<pre style="margin: 0;"> <span id="LC5865" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//save each series</span></span>
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5827
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5866
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<pre style="margin: 0;"> <span id="LC5866" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isScaleVariesEnh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">isScaleVariesEnh</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//issue363: any variation in any image</span></span>
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5867
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<pre style="margin: 0;">+<span id="LC5867" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">intenScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScale</span><span class="p">;</span></span>
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5868
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<pre style="margin: 0;">+<span id="LC5868" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">intenIntercept</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenIntercept</span><span class="p">;</span></span>
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5869
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<pre style="margin: 0;">+<span id="LC5869" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">intenScalePhilips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">;</span></span>
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5870
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<pre style="margin: 0;">+<span id="LC5870" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">RWVIntercept</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">RWVIntercept</span><span class="p">;</span></span>
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5871
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<pre style="margin: 0;">+<span id="LC5871" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">RWVScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">RWVScale</span><span class="p">;</span></span>
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5828
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5872
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<pre style="margin: 0;"> <span id="LC5872" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">series</span><span class="p">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5873
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<pre style="margin: 0;">+<span id="LC5873" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//issue461: assert these values as saveDcm2NiiCore modifies them when it applies Philips scaling</span></span>
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5874
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<pre style="margin: 0;">+<span id="LC5874" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intenScale</span><span class="p">;</span></span>
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5875
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<pre style="margin: 0;">+<span id="LC5875" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenIntercept</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intenIntercept</span><span class="p">;</span></span>
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5876
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<pre style="margin: 0;">+<span id="LC5876" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScalePhilips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intenScalePhilips</span><span class="p">;</span></span>
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5877
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<pre style="margin: 0;">+<span id="LC5877" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">RWVIntercept</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RWVIntercept</span><span class="p">;</span></span>
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5878
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<pre style="margin: 0;">+<span id="LC5878" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">RWVScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RWVScale</span><span class="p">;</span></span>
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5829
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5879
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<pre style="margin: 0;"> <span id="LC5879" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//for each volume</span></span>
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5830
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5880
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<pre style="margin: 0;"> <span id="LC5880" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gradDynVol</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span></span>
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5831
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5881
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<pre style="margin: 0;"> <span id="LC5881" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//dti4D->gradDynVol[i] = s;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5866,18 +5916,12 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis</td>
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5866
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5916
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<pre style="margin: 0;"> <span id="LC5916" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">isScaleVariesEnh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5867
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5917
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<pre style="margin: 0;"> <span id="LC5917" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">isScaleVariesEnh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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5868
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5918
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<pre style="margin: 0;"> <span id="LC5918" class="line" lang="cpp"> <span class="p">}</span></span>
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5869
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<pre style="margin: 0;">-<span id="LC5869" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//in case scale doe not vary</span></span>
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5870
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5919
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<pre style="margin: 0;"> <span id="LC5919" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">intenScale</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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5871
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5920
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<pre style="margin: 0;"> <span id="LC5920" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenIntercept</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">intenIntercept</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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5872
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5921
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<pre style="margin: 0;"> <span id="LC5921" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">intenScalePhilips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">intenScalePhilips</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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5873
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5922
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<pre style="margin: 0;"> <span id="LC5922" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">RWVIntercept</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">RWVIntercept</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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5874
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5923
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<pre style="margin: 0;"> <span id="LC5923" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">RWVScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dti4Ds</span><span class="p">.</span><span class="n" style="color: #333;">RWVScale</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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5875
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<pre style="margin: 0;">-<span id="LC5875" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//if isScaleVariesEnh</span></span>
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5876
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<pre style="margin: 0;">-<span id="LC5876" class="line" lang="cpp"> </span>
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5877
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<pre style="margin: 0;">-<span id="LC5877" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (dcmList[indx].isScaleVariesEnh) printf("Varies\n");</span></span>
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5878
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<pre style="margin: 0;">-<span id="LC5878" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (!dcmList[indx].isScaleVariesEnh) printf("no Varies\n");</span></span>
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5879
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<pre style="margin: 0;">-<span id="LC5879" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("%g %g %g\n", dcmList[indx].intenScale, dcmList[indx].intenIntercept, dcmList[indx].intenScalePhilips);</span></span>
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5880
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<pre style="margin: 0;">-<span id="LC5880" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//continue;</span></span>
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5924
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<pre style="margin: 0;">+<span id="LC5924" class="line" lang="cpp"> <span class="p">}</span></span>
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5881
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5925
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<pre style="margin: 0;"> <span id="LC5925" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">indx</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//only save bvec for first type (magnitude)</span></span>
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5882
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<td class="new_line diff-line-num" data-linenumber="5926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5926
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<pre style="margin: 0;"> <span id="LC5926" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2NiiCore</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dti4Ds</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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5883
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5927
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<pre style="margin: 0;"> <span id="LC5927" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">)</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ret2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//return EXIT_SUCCESS only if ALL are successful</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5987,14 +6031,18 @@ int isSameFloatDouble (double a, double b) {</td>
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5987
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6031
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<pre style="margin: 0;"> <span id="LC6031" class="line" lang="cpp"><span class="p">}</span></span>
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5988
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6032
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<pre style="margin: 0;"> <span id="LC6032" class="line" lang="cpp"></span>
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5989
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6033
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<pre style="margin: 0;"> <span id="LC6033" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TWarnings</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//generate a warning only once per set</span></span>
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<pre style="margin: 0;">-<span id="LC5990" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">acqNumVaries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">bitDepth</span>Varies</span><span class="p">,</span> <span class="n" style="color: #333;">dateTimeVaries</span><span class="p">,</span> <span class="n" style="color: #333;">echoVaries</span><span class="p">,</span> <span class="n" style="color: #333;">triggerVaries</span><span class="p">,</span> <span class="n" style="color: #333;">phaseVaries</span><span class="p">,</span> <span class="n" style="color: #333;">coilVaries</span><span class="p">,</span> <span class="n" style="color: #333;">forceStackSeries</span><span class="p">,</span> <span class="n" style="color: #333;">seriesUidVaries</span><span class="p">,</span> <span class="n" style="color: #333;">nameVaries</span><span class="p">,</span> <span class="n" style="color: #333;">nameEmpty</span><span class="p">,</span> <span class="n" style="color: #333;">orientVaries</span><span class="p">;</span></span>
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6034
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<pre style="margin: 0;">+<span id="LC6034" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;"><span class="idiff left">manufacturerVaries</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">modalityVaries</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">derivedVaries</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;">acqNumVaries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">dimension</span>Varies</span><span class="p">,</span> <span class="n" style="color: #333;">dateTimeVaries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">studyUidVaries</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">echoVaries</span><span class="p">,</span> <span class="n" style="color: #333;">triggerVaries</span><span class="p">,</span> <span class="n" style="color: #333;">phaseVaries</span><span class="p">,</span> <span class="n" style="color: #333;">coilVaries</span><span class="p">,</span> <span class="n" style="color: #333;">forceStackSeries</span><span class="p">,</span> <span class="n" style="color: #333;">seriesUidVaries</span><span class="p">,</span> <span class="n" style="color: #333;">nameVaries</span><span class="p">,</span> <span class="n" style="color: #333;">nameEmpty</span><span class="p">,</span> <span class="n" style="color: #333;">orientVaries</span><span class="p">;</span></span>
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6035
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<pre style="margin: 0;"> <span id="LC6035" class="line" lang="cpp"><span class="p">};</span></span>
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6036
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<pre style="margin: 0;"> <span id="LC6036" class="line" lang="cpp"></span>
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6037
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<pre style="margin: 0;"> <span id="LC6037" class="line" lang="cpp"><span class="n" style="color: #333;">TWarnings</span> <span class="n" style="color: #333;">setWarnings</span><span class="p">()</span> <span class="p">{</span></span>
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5994
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6038
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<pre style="margin: 0;"> <span id="LC6038" class="line" lang="cpp"> <span class="n" style="color: #333;">TWarnings</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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6039
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<pre style="margin: 0;">+<span id="LC6039" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">manufacturerVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6040
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<pre style="margin: 0;">+<span id="LC6040" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">modalityVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6041
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<pre style="margin: 0;">+<span id="LC6041" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">derivedVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5995
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6042
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<pre style="margin: 0;"> <span id="LC6042" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">acqNumVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5996
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<pre style="margin: 0;">-<span id="LC5996" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">bitDepth</span>Varies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6043
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<pre style="margin: 0;">+<span id="LC6043" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">dimension</span>Varies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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5997
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6044
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<pre style="margin: 0;"> <span id="LC6044" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">dateTimeVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC6045" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">studyUidVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6046
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<pre style="margin: 0;"> <span id="LC6046" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">phaseVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6047
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<pre style="margin: 0;"> <span id="LC6047" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">echoVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC6048" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">triggerVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6010,14 +6058,29 @@ TWarnings setWarnings() {</td>
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<pre style="margin: 0;"> <span id="LC6058" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isSameSet</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="n" style="color: #333;">d1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="n" style="color: #333;">d2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMopts</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TWarnings</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">warnings</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isMultiEcho</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isCoilVaries</span><span class="p">)</span> <span class="p">{</span></span>
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6011
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6059
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<pre style="margin: 0;"> <span id="LC6059" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//returns true if d1 and d2 should be stacked together as a single output</span></span>
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6012
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6060
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<pre style="margin: 0;"> <span id="LC6060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isValid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6013
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<pre style="margin: 0;">-<span id="LC6013" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isValid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6014
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<td class="new_line diff-line-num old" data-linenumber="6061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6014" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">modality</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">modality</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//do not stack MR and CT data!</span></span>
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6015
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<pre style="margin: 0;">-<span id="LC6015" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//do not stack raw and derived image types</span></span>
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6061
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<pre style="margin: 0;">+<span id="LC6061" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isValid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> </span>
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6062
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<pre style="margin: 0;">+<span id="LC6062" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isVerbose</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">seriesNum</span><span class="p">))</span> <span class="p">{</span></span>
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6063
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<pre style="margin: 0;">+<span id="LC6063" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//one would never want to combine in these situations: only raise warning for verbose modes to help troubleshooting</span></span>
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6064
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<pre style="margin: 0;">+<span id="LC6064" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturerVaries</span><span class="p">))</span> <span class="p">{</span></span>
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6065
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<pre style="margin: 0;">+<span id="LC6065" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Volumes not stacked: manufacturer varies.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6066
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<pre style="margin: 0;">+<span id="LC6066" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">manufacturerVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6067
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<pre style="margin: 0;">+<span id="LC6067" class="line" lang="cpp"> <span class="p">}</span></span>
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6068
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<pre style="margin: 0;">+<span id="LC6068" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">modality</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">modality</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">modalityVaries</span><span class="p">))</span> <span class="p">{</span></span>
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6069
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<pre style="margin: 0;">+<span id="LC6069" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Volumes not stacked: modality varies.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6070
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<pre style="margin: 0;">+<span id="LC6070" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">modalityVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6071
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<pre style="margin: 0;">+<span id="LC6071" class="line" lang="cpp"> <span class="p">}</span></span>
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6072
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<pre style="margin: 0;">+<span id="LC6072" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">derivedVaries</span><span class="p">))</span> <span class="p">{</span></span>
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6073
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<pre style="margin: 0;">+<span id="LC6073" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Volumes not stacked: derived varies.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6074
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<pre style="margin: 0;">+<span id="LC6074" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">derivedVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6075
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<pre style="margin: 0;">+<span id="LC6075" class="line" lang="cpp"> <span class="p">}</span> </span>
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6076
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<pre style="margin: 0;">+<span id="LC6076" class="line" lang="cpp"> <span class="p">}</span></span>
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6016
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6077
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<pre style="margin: 0;"> <span id="LC6077" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">manufacturer</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//do not stack data from different vendors</span></span>
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6017
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<pre style="margin: 0;">-<span id="LC6017" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForceStackSeries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6078
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<pre style="margin: 0;">+<span id="LC6078" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">modality</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">modality</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//do not stack MR and CT data!</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6079
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<pre style="margin: 0;">+<span id="LC6079" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isDerived</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//do not stack raw and derived image types</span></span>
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6080
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<pre style="margin: 0;">+<span id="LC6080" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForceStackSeries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6018
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6081
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<pre style="margin: 0;"> <span id="LC6081" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isForceStackDCE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isStackableSeries</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isStackableSeries</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">seriesNum</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">seriesNum</span><span class="p">))</span> <span class="p">{</span></span>
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6019
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6082
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<pre style="margin: 0;"> <span id="LC6082" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">forceStackSeries</span><span class="p">)</span></span>
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6020
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<td class="new_line diff-line-num old" data-linenumber="6083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6020" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">Siemens v</span>olumes stacked despite varying series number (use '-m o' to turn off merging).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6083
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<pre style="margin: 0;">+<span id="LC6083" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">V</span>olumes stacked despite varying series number (use '-m o' to turn off merging).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6021
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6084
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<pre style="margin: 0;"> <span id="LC6084" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">forceStackSeries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6022
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6085
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<pre style="margin: 0;"> <span id="LC6085" class="line" lang="cpp"> <span class="n" style="color: #333;">isForceStackSeries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6023
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6086
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<pre style="margin: 0;"> <span id="LC6086" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6048,17 +6111,29 @@ bool isSameSet (struct TDICOMdata d1, struct TDICOMdata d2, struct TDCMopts* opt</td>
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6048
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6111
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<pre style="margin: 0;"> <span id="LC6111" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isSameTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isSameFloatDouble</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">);</span></span>
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6049
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6112
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<pre style="margin: 0;"> <span id="LC6112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isSameStudyInstanceUID</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isXA10A</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isXA10A</span><span class="p">))</span></span>
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6050
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6113
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<pre style="margin: 0;"> <span id="LC6113" class="line" lang="cpp"> <span class="n" style="color: #333;">isSameTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//kludge XA10A 0008,0030 incorrect https://github.com/rordenlab/dcm2niix/issues/236</span></span>
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6051
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<pre style="margin: 0;">-<span id="LC6051" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameStudyInstanceUID</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameTime</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6052
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<pre style="margin: 0;">-<span id="LC6052" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">bitsAllocated</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">bitsAllocated</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="p">)</span> <span class="p">{</span></span>
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6053
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<pre style="margin: 0;">-<span id="LC6053" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bitDepthVaries</span><span class="p">)</span></span>
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6054
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<pre style="margin: 0;">-<span id="LC6054" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: dimensions or bit-depth varies</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6055
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<pre style="margin: 0;">-<span id="LC6055" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bitDepthVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6114
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<pre style="margin: 0;">+<span id="LC6114" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDimensionVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">xyzDim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="p">);</span></span>
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6115
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<pre style="margin: 0;">+<span id="LC6115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameStudyInstanceUID</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameTime</span><span class="p">))</span> <span class="p">{</span></span>
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6116
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<pre style="margin: 0;">+<span id="LC6116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isForceStackDCE</span><span class="p">)</span> <span class="p">{</span></span>
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6117
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<pre style="margin: 0;">+<span id="LC6117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">studyUidVaries</span><span class="p">)</span></span>
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6118
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<pre style="margin: 0;">+<span id="LC6118" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices stacked despite Study Date/Time (0008,0020;0008,0030) and Study UID (0020,000E) variation %12.12f ~= %12.12f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">);</span></span>
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6119
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<pre style="margin: 0;">+<span id="LC6119" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">studyUidVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> </span>
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6120
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<pre style="margin: 0;">+<span id="LC6120" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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6121
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<pre style="margin: 0;">+<span id="LC6121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">studyUidVaries</span><span class="p">)</span></span>
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6122
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<pre style="margin: 0;">+<span id="LC6122" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: Study Date/Time (0008,0020;0008,0030) and Study UID (0020,000E) varies %12.12f ~= %12.12f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">);</span></span>
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6123
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<pre style="margin: 0;">+<span id="LC6123" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">studyUidVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> </span>
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6124
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<pre style="margin: 0;">+<span id="LC6124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6125
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<pre style="margin: 0;">+<span id="LC6125" class="line" lang="cpp"> <span class="p">}</span></span>
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6126
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<pre style="margin: 0;">+<span id="LC6126" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6127
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<pre style="margin: 0;">+<span id="LC6127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isDimensionVaries</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6128
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<pre style="margin: 0;">+<span id="LC6128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dimensionVaries</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6129
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<pre style="margin: 0;">+<span id="LC6129" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: dimensions vary across slices</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6130
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<pre style="margin: 0;">+<span id="LC6130" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dimensionVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6056
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6131
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<pre style="margin: 0;"> <span id="LC6131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6057
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<td class="new_line diff-line-num" data-linenumber="6132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6132
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<pre style="margin: 0;"> <span id="LC6132" class="line" lang="cpp"> <span class="p">}</span></span>
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6058
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<td class="new_line diff-line-num" data-linenumber="6133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6133
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<pre style="margin: 0;"> <span id="LC6133" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifndef myIgnoreStudyTime</span></span>
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6059
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<td class="new_line diff-line-num" data-linenumber="6134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6134
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<pre style="margin: 0;"> <span id="LC6134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameTime</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//beware, some vendors incorrectly store Image Time (0008,0033) as Study Time (0008,0030).</span></span>
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6060
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<td class="new_line diff-line-num" data-linenumber="6135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6135
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<pre style="margin: 0;"> <span id="LC6135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dateTimeVaries</span><span class="p">)</span></span>
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6061
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<td class="new_line diff-line-num old" data-linenumber="6136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6061" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: Study Date/Time (0008,0020<span class="idiff left right"> / </span>0008,0030) varies %12.12f ~= %12.12f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="6062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6136
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<pre style="margin: 0;">+<span id="LC6136" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: Study Date/Time (0008,0020<span class="idiff left right">;</span>0008,0030) varies %12.12f ~= %12.12f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">dateTime</span><span class="p">);</span></span>
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6062
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<td class="new_line diff-line-num" data-linenumber="6137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6137
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<pre style="margin: 0;"> <span id="LC6137" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dateTimeVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6063
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6138
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<pre style="margin: 0;"> <span id="LC6138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6064
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6139
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<pre style="margin: 0;"> <span id="LC6139" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6070,9 +6145,9 @@ bool isSameSet (struct TDICOMdata d1, struct TDICOMdata d2, struct TDCMopts* opt</td>
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6070
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6145
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<pre style="margin: 0;"> <span id="LC6145" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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6071
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<td class="new_line diff-line-num" data-linenumber="6146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6146
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<pre style="margin: 0;"> <span id="LC6146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//we will stack these images, even if they differ in the following attributes</span></span>
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6072
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6147
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<pre style="margin: 0;"> <span id="LC6147" class="line" lang="cpp"> <span class="p">}</span></span>
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6073
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<td class="new_line diff-line-num old" data-linenumber="6148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6073" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isHasImaginary</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isHasImaginary</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isHasPhase</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isHasPhase</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p"><span class="idiff left">(</span>(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isHasReal</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isHasReal</span><span class="p">))<span class="idiff right">)</span></span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6148
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<pre style="margin: 0;">+<span id="LC6148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isHasImaginary</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isHasImaginary</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isHasPhase</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isHasPhase</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isHasReal</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">isHasReal</span><span class="p">))</span> <span class="p">{</span></span>
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6074
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<td class="new_line diff-line-num" data-linenumber="6149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6149
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<pre style="margin: 0;"> <span id="LC6149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phaseVaries</span><span class="p">)</span></span>
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6075
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<td class="new_line diff-line-num old" data-linenumber="6150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6075" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: some are phase/real/imaginary maps, others are not. Instances %d %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span><span class="p">);</span></span>
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6150
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<pre style="margin: 0;">+<span id="LC6150" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: some are phase/real/imaginary<span class="idiff left right">/phase</span> maps, others are not. Instances %d %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">imageNum</span><span class="p">);</span></span>
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6076
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<td class="new_line diff-line-num" data-linenumber="6151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6151
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<pre style="margin: 0;"> <span id="LC6151" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phaseVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6077
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6152
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<pre style="margin: 0;"> <span id="LC6152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6078
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6153
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<pre style="margin: 0;"> <span id="LC6153" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6093,11 +6168,18 @@ bool isSameSet (struct TDICOMdata d1, struct TDICOMdata d2, struct TDCMopts* opt</td>
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6093
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6168
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<pre style="margin: 0;"> <span id="LC6168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6094
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6169
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<pre style="margin: 0;"> <span id="LC6169" class="line" lang="cpp"> <span class="p">}</span></span>
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6095
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6170
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<pre style="margin: 0;"> <span id="LC6170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">coilCrc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">coilCrc</span><span class="p">)</span> <span class="p">{</span></span>
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6096
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<td class="new_line diff-line-num old" data-linenumber="6171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6096" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coilVaries</span><span class="p">)</span></span>
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6097
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<td class="new_line diff-line-num old" data-linenumber="6171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6097" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: coil varies</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6098
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<td class="new_line diff-line-num old" data-linenumber="6171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6098" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coilVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6099
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<pre style="margin: 0;">-<span id="LC6099" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isCoilVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6100
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<td class="new_line diff-line-num old" data-linenumber="6171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6171
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<pre style="margin: 0;">+<span id="LC6171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isForceStackDCE</span><span class="p">)</span> <span class="p">{</span></span>
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6172
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<pre style="margin: 0;">+<span id="LC6172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coilVaries</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6173
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<pre style="margin: 0;">+<span id="LC6173" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices stacked despite coil variation '%s' vs '%s' (use '-m o' to turn off merging)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">coilName</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">coilName</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6174
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<pre style="margin: 0;">+<span id="LC6174" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coilVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6175
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<pre style="margin: 0;">+<span id="LC6175" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isCoilVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6176
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<pre style="margin: 0;">+<span id="LC6176" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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6177
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<pre style="margin: 0;">+<span id="LC6177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coilVaries</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6178
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<pre style="margin: 0;">+<span id="LC6178" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Slices not stacked: coil varies '%s' vs '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">coilName</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">coilName</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6179
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<pre style="margin: 0;">+<span id="LC6179" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coilVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6180
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<pre style="margin: 0;">+<span id="LC6180" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isCoilVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6181
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<pre style="margin: 0;">+<span id="LC6181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6182
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<pre style="margin: 0;">+<span id="LC6182" class="line" lang="cpp"> <span class="p">}</span></span>
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6101
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6183
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<pre style="margin: 0;"> <span id="LC6183" class="line" lang="cpp"> <span class="p">}</span></span>
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6102
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6184
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<pre style="margin: 0;"> <span id="LC6184" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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6103
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6185
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<pre style="margin: 0;"> <span id="LC6185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nameEmpty</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6109,6 +6191,7 @@ bool isSameSet (struct TDICOMdata d1, struct TDICOMdata d2, struct TDCMopts* opt</td>
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6109
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6191
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<pre style="margin: 0;"> <span id="LC6191" class="line" lang="cpp"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nameVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6110
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6192
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<pre style="margin: 0;"> <span id="LC6192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6111
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6193
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<pre style="margin: 0;"> <span id="LC6193" class="line" lang="cpp"> <span class="p">}</span></span>
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6194
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<pre style="margin: 0;">+<span id="LC6194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">mosaicSlices</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//issue481</span></span>
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6112
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6195
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<pre style="margin: 0;"> <span id="LC6195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span></span>
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6113
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6196
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<pre style="margin: 0;"> <span id="LC6196" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isSameFloatGE</span><span class="p">(</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span> <span class="n" style="color: #333;">d2</span><span class="p">.</span><span class="n" style="color: #333;">orient</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span> <span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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6114
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6197
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<pre style="margin: 0;"> <span id="LC6197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">orientVaries</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">d1</span><span class="p">.</span><span class="n" style="color: #333;">isLocalizer</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6149,7 +6232,7 @@ int singleDICOM(struct TDCMopts* opts, char *fname) {</td>
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6149
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6232
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<pre style="margin: 0;"> <span id="LC6232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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6150
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6233
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<pre style="margin: 0;"> <span id="LC6233" class="line" lang="cpp"> <span class="p">}</span></span>
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6151
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6234
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<pre style="margin: 0;"> <span id="LC6234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dcmList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span><span class="p">));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6152
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<pre style="margin: 0;">-<span id="LC6152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="n" style="color: #333;">dti4D</span><span class="p">;</span></span>
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6235
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<pre style="margin: 0;">+<span id="LC6235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">dti4D</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">TDTI4D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">malloc</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">TDTI4D</span></span><span class="p"><span class="idiff right">))</span>;</span></span>
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6153
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6236
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<pre style="margin: 0;"> <span id="LC6236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TSearchList</span> <span class="n" style="color: #333;">nameList</span><span class="p">;</span></span>
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6154
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6237
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<pre style="margin: 0;"> <span id="LC6237" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// larger requires more memory, smaller more passes</span></span>
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6155
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6238
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<pre style="margin: 0;"> <span id="LC6238" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//reserve one pointer (32 or 64 bits) per potential file</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6157,84 +6240,17 @@ int singleDICOM(struct TDCMopts* opts, char *fname) {</td>
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6157
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6240
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<pre style="margin: 0;"> <span id="LC6240" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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6158
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6241
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<pre style="margin: 0;"> <span id="LC6241" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">],</span><span class="n" style="color: #333;">fname</span><span class="p">);</span></span>
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6159
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6242
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<pre style="margin: 0;"> <span id="LC6242" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">TDCMsort</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dcmSort</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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6243
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<pre style="margin: 0;">+<span id="LC6243" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">TDCMsort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dcmSort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TDCMsort</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">malloc</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TDCMsort</span></span><span class="p"><span class="idiff right">))</span>;</span></span>
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6161
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6244
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<pre style="margin: 0;"> <span id="LC6244" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">converted2NII</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6162
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<td class="new_line diff-line-num old" data-linenumber="6245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6162" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDICOMv</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressFlag</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//ignore compile warning - memory only freed on first of 2 passes</span></span>
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6245
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<pre style="margin: 0;">+<span id="LC6245" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDICOMv</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressFlag</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//ignore compile warning - memory only freed on first of 2 passes</span></span>
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6163
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6246
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<pre style="margin: 0;"> <span id="LC6246" class="line" lang="cpp"> <span class="n" style="color: #333;">fillTDCMsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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6164
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<pre style="margin: 0;">-<span id="LC6164" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6247
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<pre style="margin: 0;">+<span id="LC6247" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6165
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6248
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<pre style="margin: 0;"> <span id="LC6248" class="line" lang="cpp"> <span class="n" style="color: #333;">freeNameList</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">);</span></span>
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6166
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<pre style="margin: 0;">-<span id="LC6166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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6167
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<pre style="margin: 0;">-<span id="LC6167" class="line" lang="cpp"><span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">// singleDICOM()</span></span>
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6168
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<pre style="margin: 0;">-<span id="LC6168" class="line" lang="cpp"></span>
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6169
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<pre style="margin: 0;">-<span id="LC6169" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef myTextFileInputLists //https://github.com/rordenlab/dcm2niix/issues/288</span></span>
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6170
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<pre style="margin: 0;">-<span id="LC6170" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">textDICOM</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMopts</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fname</span><span class="p">)</span> <span class="p">{</span></span>
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6171
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<pre style="margin: 0;">-<span id="LC6171" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//check input file</span></span>
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6172
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<pre style="margin: 0;">-<span id="LC6172" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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6173
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<pre style="margin: 0;">-<span id="LC6173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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6174
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<pre style="margin: 0;">-<span id="LC6174" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USING_R</span></span>
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6175
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<pre style="margin: 0;">-<span id="LC6175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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6176
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6176" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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6177
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6177" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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6178
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6178" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6179
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6179" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6180
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6180" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="mi" style="color: #099;">2048</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6181
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fgets</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">),</span> <span class="n" style="color: #333;">fp</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6182
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6182" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6183
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Unix LF</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6184
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6184" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\r'</span><span class="p">)</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Windows CR/LF</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6185
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6185" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (isDICOMfile(dcmname) == 0) { //<- this will reject DICOM metadata not wrapped with a header</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6186
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6186" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is_fileexists</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is_fileNotDir</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">))</span> <span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//<-this will accept meta data</span></span>
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6187
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6187" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6188
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6188" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Problem with file '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">dcmname</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6189
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<pre style="margin: 0;">-<span id="LC6189" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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6190
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<pre style="margin: 0;">-<span id="LC6190" class="line" lang="cpp"> <span class="p">}</span></span>
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6191
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6191" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf("%s\n", dcmname);</span></span>
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6192
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<pre style="margin: 0;">-<span id="LC6192" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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6193
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<pre style="margin: 0;">-<span id="LC6193" class="line" lang="cpp"> <span class="p">}</span></span>
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6194
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<pre style="margin: 0;">-<span id="LC6194" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6195
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<pre style="margin: 0;">-<span id="LC6195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6196
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6196" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"No DICOM files found '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">dcmname</span><span class="p">);</span></span>
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6197
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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6198
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6198" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6199
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6199" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Found %d DICOM file(s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nConvert</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6200
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6200" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifndef USING_R</span></span>
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6201
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<pre style="margin: 0;">-<span id="LC6201" class="line" lang="cpp"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//show immediately if run from MRIcroGL GUI</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6202
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6202" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6203
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6203" class="line" lang="cpp"> <span class="n" style="color: #333;">TDCMsort</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dcmSort</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">TDCMsort</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">TDCMsort</span><span class="p">));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6204
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<pre style="margin: 0;">-<span id="LC6204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dcmList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span><span class="p">));</span></span>
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6205
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<pre style="margin: 0;">-<span id="LC6205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="n" style="color: #333;">dti4D</span><span class="p">;</span></span>
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6206
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TSearchList</span> <span class="n" style="color: #333;">nameList</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6207
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6207" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nConvert</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// larger requires more memory, smaller more passes</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6208
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6208" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//reserve one pointer (32 or 64 bits) per potential file</span></span>
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6209
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<pre style="margin: 0;">-<span id="LC6209" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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6210
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<pre style="margin: 0;">-<span id="LC6210" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6211
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<pre style="margin: 0;">-<span id="LC6211" class="line" lang="cpp"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6212
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<pre style="margin: 0;">-<span id="LC6212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fgets</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">),</span> <span class="n" style="color: #333;">fp</span><span class="p">))</span> <span class="p">{</span></span>
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6213
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<pre style="margin: 0;">-<span id="LC6213" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6214
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Unix LF</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6215
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\r'</span><span class="p">)</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Windows CR/LF</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6216
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6216" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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6217
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6217" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">],</span><span class="n" style="color: #333;">dcmname</span><span class="p">);</span></span>
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6218
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6218" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6219
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6219" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">nConvert</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDICOMv</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">nConvert</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressFlag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//ignore compile warning - memory only freed on first of 2 passes</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6220
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<pre style="margin: 0;">-<span id="LC6220" class="line" lang="cpp"> <span class="n" style="color: #333;">fillTDCMsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="n" style="color: #333;">nConvert</span><span class="p">],</span> <span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">nConvert</span><span class="p">]);</span></span>
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6221
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<pre style="margin: 0;">-<span id="LC6221" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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6222
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<pre style="margin: 0;">-<span id="LC6222" class="line" lang="cpp"> <span class="p">}</span></span>
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6223
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6223" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6224
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6224" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMsort</span><span class="p">),</span> <span class="n" style="color: #333;">compareTDCMsort</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//sort based on series and image numbers....</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6225
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<td class="new_line diff-line-num old" data-linenumber="6249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6225" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6226
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<pre style="margin: 0;">-<span id="LC6226" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">);</span></span>
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6249
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<pre style="margin: 0;">+<span id="LC6249" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6250
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<pre style="margin: 0;">+<span id="LC6250" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">);</span></span>
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6227
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6251
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<pre style="margin: 0;"> <span id="LC6251" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">);</span></span>
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6228
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<pre style="margin: 0;">-<span id="LC6228" class="line" lang="cpp"> <span class="n" style="color: #333;">freeNameList</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC6252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6230" class="line" lang="cpp"><span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">//textDICOM()</span></span>
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6231
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<pre style="margin: 0;">-<span id="LC6231" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC6232" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else //ifdef myTextFileInputLists</span></span>
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6233
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<pre style="margin: 0;">-<span id="LC6233" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">textDICOM</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMopts</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fname</span><span class="p">)</span> <span class="p">{</span></span>
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6234
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<pre style="margin: 0;">-<span id="LC6234" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to parse txt files: re-compile with 'myTextFileInputLists' (see issue 288)"</span><span class="p">);</span></span>
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6235
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<pre style="margin: 0;">-<span id="LC6235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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6236
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<pre style="margin: 0;">-<span id="LC6236" class="line" lang="cpp"><span class="p">}</span></span>
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6237
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<pre style="margin: 0;">-<span id="LC6237" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC6253" class="line" lang="cpp"><span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">// singleDICOM()</span></span>
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<pre style="margin: 0;"> <span id="LC6254" class="line" lang="cpp"></span>
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6255
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<pre style="margin: 0;"> <span id="LC6255" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">fileBytes</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fname</span><span class="p">)</span> <span class="p">{</span></span>
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6256
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<pre style="margin: 0;"> <span id="LC6256" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6337,12 +6353,13 @@ int convert_parRec(char * fnm, struct TDCMopts opts) {</td>
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6353
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<pre style="margin: 0;"> <span id="LC6353" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">fnm</span><span class="p">);</span></span>
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6354
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<pre style="margin: 0;"> <span id="LC6354" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//nameList.str[0] = (char *)malloc(strlen(opts.indir)+1);</span></span>
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6339
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6355
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<pre style="margin: 0;"> <span id="LC6355" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//strcpy(nameList.str[0],opts.indir);</span></span>
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<pre style="margin: 0;">-<span id="LC6340" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">TDTI4D</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dti4D</span></span><span class="p">;</span></span>
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6341
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<pre style="margin: 0;">-<span id="LC6341" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nii_readParRec</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">dti4D</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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6356
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<pre style="margin: 0;">+<span id="LC6356" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">TDTI4D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">dti4D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">TDTI4D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">malloc</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">TDTI4D</span></span><span class="p"><span class="idiff right">))</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC6357" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nii_readParRec</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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6342
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6358
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<pre style="margin: 0;"> <span id="LC6358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMsort</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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6343
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6359
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<pre style="margin: 0;"> <span id="LC6359" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">indx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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6344
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6360
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<pre style="margin: 0;"> <span id="LC6360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">isValid</span><span class="p">)</span></span>
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6345
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<pre style="margin: 0;">-<span id="LC6345" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6361
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<pre style="margin: 0;">+<span id="LC6361" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6362
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<pre style="margin: 0;">+<span id="LC6362" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6346
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6363
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<pre style="margin: 0;"> <span id="LC6363" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//if (nConvertTotal == 0)</span></span>
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6347
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6364
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<pre style="margin: 0;"> <span id="LC6364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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6348
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6365
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<pre style="margin: 0;"> <span id="LC6365" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"No valid PAR/REC files were found</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6599,25 +6616,57 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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6599
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6616
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<pre style="margin: 0;"> <span id="LC6616" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef myTimer</span></span>
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6600
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6617
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<pre style="margin: 0;"> <span id="LC6617" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">clock_t</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clock</span><span class="p">();</span></span>
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6601
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6618
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<pre style="margin: 0;"> <span id="LC6618" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6602
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<pre style="margin: 0;">-<span id="LC6602" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//1: find filenames of dicom files: up to two passes if we found more files than we allocated memory</span></span>
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6603
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<pre style="margin: 0;">-<span id="LC6603" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span> <span class="p">{</span></span>
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6604
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<pre style="margin: 0;">-<span id="LC6604" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//reserve one pointer (32 or 64 bits) per potential file</span></span>
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<pre style="margin: 0;">-<span id="LC6605" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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6606
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<pre style="margin: 0;">-<span id="LC6606" class="line" lang="cpp"> <span class="n" style="color: #333;">searchDirForDICOM</span><span class="p">(</span><span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dirSearchDepth</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">);</span></span>
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6607
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<pre style="margin: 0;">-<span id="LC6607" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="p">)</span></span>
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6608
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<pre style="margin: 0;">-<span id="LC6608" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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6609
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<pre style="margin: 0;">-<span id="LC6609" class="line" lang="cpp"> <span class="n" style="color: #333;">freeNameList</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">);</span></span>
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6610
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<pre style="margin: 0;">-<span id="LC6610" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6611
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<pre style="margin: 0;">-<span id="LC6611" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("Second pass required, found %ld images\n", nameList.numItems);</span></span>
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6612
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<pre style="margin: 0;">-<span id="LC6612" class="line" lang="cpp"> <span class="p">}</span></span>
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6613
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<pre style="margin: 0;">-<span id="LC6613" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6614
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<pre style="margin: 0;">-<span id="LC6614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dirSearchDepth</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6615
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<pre style="margin: 0;">-<span id="LC6615" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to find any DICOM images in %s (or subfolders %d deep)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dirSearchDepth</span><span class="p">);</span></span>
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6616
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<pre style="margin: 0;">-<span id="LC6616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">//keep silent for dirSearchDepth = 0 - presumably searching multiple folders</span></span>
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6617
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<pre style="margin: 0;">-<span id="LC6617" class="line" lang="cpp"> <span class="p">{};</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6618
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<pre style="margin: 0;">-<span id="LC6618" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//ignore compile warning - memory only freed on first of 2 passes</span></span>
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6619
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<pre style="margin: 0;">-<span id="LC6619" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kEXIT_NO_VALID_FILES_FOUND</span><span class="p">;</span></span>
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6620
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<pre style="margin: 0;">-<span id="LC6620" class="line" lang="cpp"> <span class="p">}</span></span>
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6619
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<pre style="margin: 0;">+<span id="LC6619" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">is_fileNotDir</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indir</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isExt</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="s" style="color: #d14;">".txt"</span><span class="p">)</span> <span class="p">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="6621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6620
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<pre style="margin: 0;">+<span id="LC6620" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//reserve one pointer (32 or 64 bits) per potential file</span></span>
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6621
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<pre style="margin: 0;">+<span id="LC6621" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6622
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<pre style="margin: 0;">+<span id="LC6622" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//textDICOM</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6623
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<pre style="margin: 0;">+<span id="LC6623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6624
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<pre style="margin: 0;">+<span id="LC6624" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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6625
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<pre style="margin: 0;">+<span id="LC6625" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="mi" style="color: #099;">2048</span><span class="p">];</span></span>
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6626
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<pre style="margin: 0;">+<span id="LC6626" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fgets</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">),</span> <span class="n" style="color: #333;">fp</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6627
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<pre style="margin: 0;">+<span id="LC6627" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6628
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<pre style="margin: 0;">+<span id="LC6628" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Unix LF</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6629
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<pre style="margin: 0;">+<span id="LC6629" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\r'</span><span class="p">)</span> <span class="n" style="color: #333;">dcmname</span><span class="p">[</span><span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Windows CR/LF</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6630
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<pre style="margin: 0;">+<span id="LC6630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is_fileexists</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is_fileNotDir</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">))</span> <span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//<-this will accept meta data</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6631
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<pre style="margin: 0;">+<span id="LC6631" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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6632
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<pre style="margin: 0;">+<span id="LC6632" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Problem with file '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">dcmname</span><span class="p">);</span></span>
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6633
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<pre style="margin: 0;">+<span id="LC6633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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6634
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<pre style="margin: 0;">+<span id="LC6634" class="line" lang="cpp"> <span class="p">}</span></span>
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6635
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<pre style="margin: 0;">+<span id="LC6635" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6636
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<pre style="margin: 0;">+<span id="LC6636" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">dcmname</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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6637
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<pre style="margin: 0;">+<span id="LC6637" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">],</span><span class="n" style="color: #333;">dcmname</span><span class="p">);</span></span>
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6638
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<pre style="margin: 0;">+<span id="LC6638" class="line" lang="cpp"> <span class="p">}</span></span>
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6639
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<pre style="margin: 0;">+<span id="LC6639" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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6640
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<pre style="margin: 0;">+<span id="LC6640" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6641
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<pre style="margin: 0;">+<span id="LC6641" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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6642
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<pre style="margin: 0;">+<span id="LC6642" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6643" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Too many file names in '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indir</span><span class="p">);</span></span>
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6644
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<pre style="margin: 0;">+<span id="LC6644" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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6645
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<pre style="margin: 0;">+<span id="LC6645" class="line" lang="cpp"> <span class="p">}</span></span>
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6646
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<pre style="margin: 0;">+<span id="LC6646" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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6647
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<pre style="margin: 0;">+<span id="LC6647" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kEXIT_NO_VALID_FILES_FOUND</span><span class="p">;</span></span>
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6648
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<pre style="margin: 0;">+<span id="LC6648" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Found %lu files in '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indir</span><span class="p">);</span></span>
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6649
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<pre style="margin: 0;">+<span id="LC6649" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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6650
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<pre style="margin: 0;">+<span id="LC6650" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//1: find filenames of dicom files: up to two passes if we found more files than we allocated memory</span></span>
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6651
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<pre style="margin: 0;">+<span id="LC6651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span> <span class="p">{</span></span>
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6652
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<pre style="margin: 0;">+<span id="LC6652" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//reserve one pointer (32 or 64 bits) per potential file</span></span>
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6653
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<pre style="margin: 0;">+<span id="LC6653" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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6654
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<pre style="margin: 0;">+<span id="LC6654" class="line" lang="cpp"> <span class="n" style="color: #333;">searchDirForDICOM</span><span class="p">(</span><span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dirSearchDepth</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">);</span></span>
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6655
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<pre style="margin: 0;">+<span id="LC6655" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span><span class="p">)</span></span>
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6656
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<pre style="margin: 0;">+<span id="LC6656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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6657
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<pre style="margin: 0;">+<span id="LC6657" class="line" lang="cpp"> <span class="n" style="color: #333;">freeNameList</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">);</span></span>
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6658
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<pre style="margin: 0;">+<span id="LC6658" class="line" lang="cpp"> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">maxItems</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6659
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<pre style="margin: 0;">+<span id="LC6659" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printMessage("Second pass required, found %ld images\n", nameList.numItems);</span></span>
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6660
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<pre style="margin: 0;">+<span id="LC6660" class="line" lang="cpp"> <span class="p">}</span></span>
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6661
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<pre style="margin: 0;">+<span id="LC6661" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dirSearchDepth</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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6663
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<pre style="margin: 0;">+<span id="LC6663" class="line" lang="cpp"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to find any DICOM images in %s (or subfolders %d deep)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dirSearchDepth</span><span class="p">);</span></span>
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6664
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<pre style="margin: 0;">+<span id="LC6664" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">//keep silent for dirSearchDepth = 0 - presumably searching multiple folders</span></span>
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6665
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<pre style="margin: 0;">+<span id="LC6665" class="line" lang="cpp"> <span class="p">{};</span></span>
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6666
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<pre style="margin: 0;">+<span id="LC6666" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//ignore compile warning - memory only freed on first of 2 passes</span></span>
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6667
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<pre style="margin: 0;">+<span id="LC6667" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kEXIT_NO_VALID_FILES_FOUND</span><span class="p">;</span></span>
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6668
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<pre style="margin: 0;">+<span id="LC6668" class="line" lang="cpp"> <span class="p">}</span></span>
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6669
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<pre style="margin: 0;">+<span id="LC6669" class="line" lang="cpp"> <span class="p">}</span></span>
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6621
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6670
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<pre style="margin: 0;"> <span id="LC6670" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nDcm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">;</span></span>
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6622
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6671
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<pre style="margin: 0;"> <span id="LC6671" class="line" lang="cpp"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span> <span class="s" style="color: #d14;">"Found %lu DICOM file(s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//includes images and other non-image DICOMs</span></span>
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6623
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6672
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<pre style="margin: 0;"> <span id="LC6672" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef myTimer</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6628,7 +6677,7 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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6628
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6677
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<pre style="margin: 0;"> <span id="LC6677" class="line" lang="cpp"> <span class="n" style="color: #333;">progressPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reportProgress</span><span class="p">(</span><span class="n" style="color: #333;">progressPct</span><span class="p">,</span> <span class="n" style="color: #333;">kStage1Frac</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//proportion correct, 0..100</span></span>
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6629
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6678
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<pre style="margin: 0;"> <span id="LC6678" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// struct TDICOMdata dcmList [nameList.numItems]; //<- this exhausts the stack for large arrays</span></span>
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6630
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6679
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<pre style="margin: 0;"> <span id="LC6679" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dcmList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">numItems</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDICOMdata</span><span class="p">));</span></span>
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6631
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<pre style="margin: 0;">-<span id="LC6631" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="n" style="color: #333;">dti4D</span><span class="p">;</span></span>
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6680
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<pre style="margin: 0;">+<span id="LC6680" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDTI4D</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">dti4D</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">TDTI4D</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">malloc</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">TDTI4D</span></span><span class="p"><span class="idiff right">))</span>;</span></span>
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6632
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6681
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<pre style="margin: 0;"> <span id="LC6681" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nConvertTotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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6633
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6682
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<pre style="margin: 0;"> <span id="LC6682" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">compressionWarning</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6634
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6683
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<pre style="margin: 0;"> <span id="LC6683" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">convertError</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6647,13 +6696,15 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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<pre style="margin: 0;"> <span id="LC6696" class="line" lang="cpp"> <span class="n" style="color: #333;">convertError</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC6697" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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6698
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<pre style="margin: 0;"> <span id="LC6698" class="line" lang="cpp"> <span class="p">}</span></span>
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6650
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<pre style="margin: 0;">-<span id="LC6650" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDICOMv</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressFlag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//ignore compile warning - memory only freed on first of 2 passes</span></span>
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6651
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<pre style="margin: 0;">-<span id="LC6651" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (!dcmList[i].isValid) printf(">>>>Not a valid DICOM %s\n", nameList.str[i]);</span></span>
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6652
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<pre style="margin: 0;">-<span id="LC6652" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">isValid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">dti4D</span><span class="p">.</span><span class="n" style="color: #333;">sliceOrder</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//4D dataset: dti4D arrays require huge amounts of RAM - write this immediately</span></span>
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6699
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<pre style="margin: 0;">+<span id="LC6699" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDICOMv</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressFlag</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//ignore compile warning - memory only freed on first of 2 passes</span></span>
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<pre style="margin: 0;">+<span id="LC6700" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isIgnoreSeriesInstanceUID</span><span class="p">)</span></span>
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6701
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<pre style="margin: 0;">+<span id="LC6701" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seriesUidCrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seriesNum</span><span class="p">;</span></span>
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6702
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<pre style="margin: 0;">+<span id="LC6702" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (!dcmList[i].isValid) printf(">>>>Not a valid DICOM %s\n", nameList.str[i]);</span></span>
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6703
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<pre style="margin: 0;">+<span id="LC6703" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">isValid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">dti4D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sliceOrder</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">numDti</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//4D dataset: dti4D arrays require huge amounts of RAM - write this immediately</span></span>
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6653
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6704
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<pre style="margin: 0;"> <span id="LC6704" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMsort</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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6654
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6705
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<pre style="margin: 0;"> <span id="LC6705" class="line" lang="cpp"> <span class="n" style="color: #333;">fillTDCMsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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6655
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6706
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<pre style="margin: 0;"> <span id="LC6706" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">converted2NII</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6656
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<pre style="margin: 0;">-<span id="LC6656" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC6707" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6657
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6708
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<pre style="margin: 0;"> <span id="LC6708" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">)</span></span>
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6658
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6709
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<pre style="margin: 0;"> <span id="LC6709" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvertTotal</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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6659
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6710
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<pre style="margin: 0;"> <span id="LC6710" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6671,7 +6722,9 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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6671
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<td class="new_line diff-line-num" data-linenumber="6722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6722
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<pre style="margin: 0;"> <span id="LC6722" class="line" lang="cpp"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clock</span><span class="p">();</span></span>
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6672
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6723
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<pre style="margin: 0;"> <span id="LC6723" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6673
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<td class="new_line diff-line-num" data-linenumber="6724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6724
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<pre style="margin: 0;"> <span id="LC6724" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isRenameNotConvert</span><span class="p">)</span> <span class="p">{</span></span>
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6674
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<td class="new_line diff-line-num old" data-linenumber="6725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6674" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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6725
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<pre style="margin: 0;">+<span id="LC6725" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">);</span></span>
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6726
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<pre style="margin: 0;">+<span id="LC6726" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6727
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<pre style="margin: 0;">+<span id="LC6727" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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6675
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6728
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<pre style="margin: 0;"> <span id="LC6728" class="line" lang="cpp"> <span class="p">}</span></span>
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6676
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6729
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<pre style="margin: 0;"> <span id="LC6729" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USING_R</span></span>
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6677
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6730
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<pre style="margin: 0;"> <span id="LC6730" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isScanOnly</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6728,8 +6781,8 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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6728
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6781
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<pre style="margin: 0;"> <span id="LC6781" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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6729
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6782
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<pre style="margin: 0;"> <span id="LC6782" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">nDcm</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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6730
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6783
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<pre style="margin: 0;"> <span id="LC6783" class="line" lang="cpp"> <span class="n" style="color: #333;">isMultiEcho</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6731
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<pre style="margin: 0;">-<span id="LC6731" class="line" lang="cpp"> <span class="n" style="color: #333;">isNonParallelSlices</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6732
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6784
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<pre style="margin: 0;"> <span id="LC6784" class="line" lang="cpp"> <span class="n" style="color: #333;">isCoilVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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6785
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<pre style="margin: 0;">+<span id="LC6785" class="line" lang="cpp"> <span class="n" style="color: #333;">isNonParallelSlices</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> </span>
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6733
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6786
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<pre style="margin: 0;"> <span id="LC6786" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSameSet</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">warnings</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isMultiEcho</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isCoilVaries</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="6734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6734
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<td class="new_line diff-line-num" data-linenumber="6787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6787
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<pre style="margin: 0;"> <span id="LC6787" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">converted2NII</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//do not reprocess repeats</span></span>
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6735
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6788
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<pre style="margin: 0;"> <span id="LC6788" class="line" lang="cpp"> <span class="n" style="color: #333;">fillTDCMsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="n" style="color: #333;">nConvert</span><span class="p">],</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6756,7 +6809,7 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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6756
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6809
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<pre style="margin: 0;"> <span id="LC6809" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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6757
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<td class="new_line diff-line-num" data-linenumber="6810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6810
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<pre style="margin: 0;"> <span id="LC6810" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//nConvert = removeDuplicatesVerbose(nConvert, dcmSort, &nameList);</span></span>
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<td class="old_line diff-line-num" data-linenumber="6758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6758
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<td class="new_line diff-line-num" data-linenumber="6811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6811
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<pre style="margin: 0;"> <span id="LC6811" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeDuplicates</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6759
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<td class="new_line diff-line-num old" data-linenumber="6812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6759" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6812
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<pre style="margin: 0;">+<span id="LC6812" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6760
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6813
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<pre style="margin: 0;"> <span id="LC6813" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">)</span></span>
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6761
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6814
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<pre style="margin: 0;"> <span id="LC6814" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvertTotal</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">nConvert</span><span class="p">;</span></span>
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6762
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6815
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<pre style="margin: 0;"> <span id="LC6815" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6792,6 +6845,25 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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6792
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6845
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<pre style="margin: 0;"> <span id="LC6845" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvert</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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6793
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6846
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<pre style="margin: 0;"> <span id="LC6846" class="line" lang="cpp"> <span class="p">}</span></span>
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6794
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<td class="new_line diff-line-num" data-linenumber="6847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6847
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<pre style="margin: 0;"> <span id="LC6847" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//for all images with same seriesUID as first one</span></span>
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<td class="old_line diff-line-num new" data-linenumber="6795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6848
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<pre style="margin: 0;">+<span id="LC6848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isNonParallelSlices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">CSA</span><span class="p">.</span><span class="n" style="color: #333;">mosaicSlices</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//issue481: if ANY volumes are non-parallel, save ALL as 3D</span></span>
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<td class="old_line diff-line-num new" data-linenumber="6795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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6849
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<pre style="margin: 0;">+<span id="LC6849" class="line" lang="cpp"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Saving mosaics with non-parallel slices as 3D (issue 481)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6850
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<pre style="margin: 0;">+<span id="LC6850" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">nDcm</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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6851
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<pre style="margin: 0;">+<span id="LC6851" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ji</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crcSort</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">indx</span><span class="p">;</span></span>
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6852
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<pre style="margin: 0;">+<span id="LC6852" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">seriesUidCrc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">ji</span><span class="p">].</span><span class="n" style="color: #333;">seriesUidCrc</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> </span>
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6853
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<pre style="margin: 0;">+<span id="LC6853" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">ji</span><span class="p">].</span><span class="n" style="color: #333;">converted2NII</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6854
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<pre style="margin: 0;">+<span id="LC6854" class="line" lang="cpp"> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">ji</span><span class="p">].</span><span class="n" style="color: #333;">isNonParallelSlices</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6855
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<pre style="margin: 0;">+<span id="LC6855" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isMultiEcho</span><span class="p">)</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">ji</span><span class="p">].</span><span class="n" style="color: #333;">isMultiEcho</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6856
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<pre style="margin: 0;">+<span id="LC6856" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isCoilVaries</span><span class="p">)</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">ji</span><span class="p">].</span><span class="n" style="color: #333;">isCoilVaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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6857
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<pre style="margin: 0;">+<span id="LC6857" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TDCMsort</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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6858
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<pre style="margin: 0;">+<span id="LC6858" class="line" lang="cpp"> <span class="n" style="color: #333;">fillTDCMsort</span><span class="p">(</span><span class="n" style="color: #333;">dcmSort</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">ji</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">[</span><span class="n" style="color: #333;">ji</span><span class="p">]);</span></span>
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6859
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<pre style="margin: 0;">+<span id="LC6859" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6860
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<pre style="margin: 0;">+<span id="LC6860" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">)</span></span>
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6861
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<pre style="margin: 0;">+<span id="LC6861" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvertTotal</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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6862
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<pre style="margin: 0;">+<span id="LC6862" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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6863
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<pre style="margin: 0;">+<span id="LC6863" class="line" lang="cpp"> <span class="n" style="color: #333;">convertError</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> </span>
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6864
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<pre style="margin: 0;">+<span id="LC6864" class="line" lang="cpp"> <span class="p">}</span></span>
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6865
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<pre style="margin: 0;">+<span id="LC6865" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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6866
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<pre style="margin: 0;">+<span id="LC6866" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//issue481</span></span>
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6795
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6867
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<pre style="margin: 0;"> <span id="LC6867" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//issue 381: ensure all images are informed if there are variations in echo, parallel slices, coil name:</span></span>
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6796
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6868
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<pre style="margin: 0;"> <span id="LC6868" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isMultiEcho</span><span class="p">)</span></span>
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6797
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6869
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<pre style="margin: 0;"> <span id="LC6869" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">jMax</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6816,7 +6888,7 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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6816
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6888
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<pre style="margin: 0;"> <span id="LC6888" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeDuplicatesVerbose</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="6817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6817
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6889
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<pre style="margin: 0;"> <span id="LC6889" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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6818
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6890
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<pre style="margin: 0;"> <span id="LC6890" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeDuplicates</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6819
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<td class="new_line diff-line-num old" data-linenumber="6891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6819" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="6820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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6891
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<pre style="margin: 0;">+<span id="LC6891" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saveDcm2Nii</span><span class="p">(</span><span class="n" style="color: #333;">nConvert</span><span class="p">,</span> <span class="n" style="color: #333;">dcmSort</span><span class="p">,</span> <span class="n" style="color: #333;">dcmList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nameList</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6820
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6892
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<pre style="margin: 0;"> <span id="LC6892" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="6821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6821
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6893
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<pre style="margin: 0;"> <span id="LC6893" class="line" lang="cpp"> <span class="n" style="color: #333;">nConvertTotal</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">nConvert</span><span class="p">;</span></span>
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6822
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6894
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<pre style="margin: 0;"> <span id="LC6894" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6837,6 +6909,7 @@ int nii_loadDirCore(char *indir, struct TDCMopts* opts) {</td>
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6837
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6909
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<pre style="margin: 0;"> <span id="LC6909" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="old_line diff-line-num" data-linenumber="6838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6838
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6910
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<pre style="margin: 0;"> <span id="LC6910" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isProgress</span><span class="p">)</span> <span class="n" style="color: #333;">progressPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reportProgress</span><span class="p">(</span><span class="n" style="color: #333;">progressPct</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//proportion correct, 0..100</span></span>
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<td class="old_line diff-line-num" data-linenumber="6839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6839
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<td class="new_line diff-line-num" data-linenumber="6911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6911
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<pre style="margin: 0;"> <span id="LC6911" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dcmList</span><span class="p">);</span></span>
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6912
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<pre style="margin: 0;">+<span id="LC6912" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dti4D</span><span class="p">);</span></span>
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6840
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6913
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<pre style="margin: 0;"> <span id="LC6913" class="line" lang="cpp"> <span class="n" style="color: #333;">freeNameList</span><span class="p">(</span><span class="n" style="color: #333;">nameList</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="6841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6841
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6914
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<pre style="margin: 0;"> <span id="LC6914" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">convertError</span><span class="p">)</span> <span class="p">{</span></span>
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6842
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6915
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<pre style="margin: 0;"> <span id="LC6915" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nConvertTotal</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6955,8 +7028,10 @@ int nii_loadDir(struct TDCMopts* opts) {</td>
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6955
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7028
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<pre style="margin: 0;"> <span id="LC7028" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">convert_parRec</span><span class="p">(</span><span class="n" style="color: #333;">pname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opts</span><span class="p">);</span></span>
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6956
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<td class="new_line diff-line-num" data-linenumber="7029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7029
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<pre style="margin: 0;"> <span id="LC7029" class="line" lang="cpp"> <span class="p">};</span></span>
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6957
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7030
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<pre style="margin: 0;"> <span id="LC7030" class="line" lang="cpp"> <span class="p">}</span></span>
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6958
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<pre style="margin: 0;">-<span id="LC6958" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isFile</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isOnlySingleFile</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isExt</span><span class="p">(</span><span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="s" style="color: #d14;">".txt"</span><span class="p">)</span> <span class="p">)</span></span>
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6959
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<td class="new_line diff-line-num old" data-linenumber="7031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">textDICOM</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">indir</span><span class="p">);</span></span>
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7031
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<pre style="margin: 0;">+<span id="LC7031" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isFile</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isOnlySingleFile</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isExt</span><span class="p">(</span><span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="s" style="color: #d14;">".txt"</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7032
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<pre style="margin: 0;">+<span id="LC7032" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indir</span><span class="p">,</span><span class="n" style="color: #333;">indir</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7033
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<pre style="margin: 0;">+<span id="LC7033" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nii_loadDirCore</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">);</span></span>
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7034
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<pre style="margin: 0;">+<span id="LC7034" class="line" lang="cpp"> <span class="p">}</span></span>
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6960
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<td class="new_line diff-line-num" data-linenumber="7035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7035
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<pre style="margin: 0;"> <span id="LC7035" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isRenameNotConvert</span><span class="p">)</span> <span class="p">{</span></span>
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6961
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<td class="new_line diff-line-num" data-linenumber="7036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7036
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<pre style="margin: 0;"> <span id="LC7036" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">searchDirRenameDICOM</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indir</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dirSearchDepth</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">);</span></span>
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6962
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<td class="new_line diff-line-num" data-linenumber="7037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7037
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<pre style="margin: 0;"> <span id="LC7037" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nConvert</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kEXIT_RENAME_ERROR</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7163,6 +7238,7 @@ void setDefaultOpts (struct TDCMopts *opts, const char * argv[]) { //either "set</td>
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7163
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<td class="new_line diff-line-num" data-linenumber="7238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7238
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<pre style="margin: 0;"> <span id="LC7238" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isRenameNotConvert</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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7164
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<td class="new_line diff-line-num" data-linenumber="7239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7239
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<pre style="margin: 0;"> <span id="LC7239" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isForceStackSameSeries</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//automatic: stack CTs, do not stack MRI</span></span>
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<td class="old_line diff-line-num" data-linenumber="7165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7165
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<td class="new_line diff-line-num" data-linenumber="7240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7240
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<pre style="margin: 0;"> <span id="LC7240" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isForceStackDCE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7241
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<pre style="margin: 0;">+<span id="LC7241" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isIgnoreSeriesInstanceUID</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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7166
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<td class="new_line diff-line-num" data-linenumber="7242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7242
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<pre style="margin: 0;"> <span id="LC7242" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isIgnoreDerivedAnd2D</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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7167
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<td class="new_line diff-line-num" data-linenumber="7243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7243
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<pre style="margin: 0;"> <span id="LC7243" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isForceOnsetTimes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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7168
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<td class="new_line diff-line-num" data-linenumber="7244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7244
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<pre style="margin: 0;"> <span id="LC7244" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isPhilipsFloatNotDisplayScaling</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#005a4e3188aea73fb4081e076e27f916ad6ee193"><strong>console/nii_dicom_batch.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,7 +35,7 @@ extern "C" {</td>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_NUM_SERIES 16</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">TDCMopts</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isTestx0021x105E</span><span class="p">,</span> <span class="n" style="color: #333;">isAddNamePostFixes</span><span class="p">,</span> <span class="n" style="color: #333;">isSaveNativeEndian</span><span class="p">,</span> <span class="n" style="color: #333;">isSaveNRRD</span><span class="p">,</span> <span class="n" style="color: #333;">isOneDirAtATime</span><span class="p">,</span> <span class="n" style="color: #333;">isRenameNotConvert</span><span class="p">,</span> <span class="n" style="color: #333;">isSave3D</span><span class="p">,</span> <span class="n" style="color: #333;">isGz</span><span class="p">,</span> <span class="n" style="color: #333;">isPipedGz</span><span class="p">,</span> <span class="n" style="color: #333;">isFlipY</span><span class="p">,</span> <span class="n" style="color: #333;">isCreateBIDS</span><span class="p">,</span> <span class="n" style="color: #333;">isSortDTIbyBVal</span><span class="p">,</span> <span class="n" style="color: #333;">isAnonymizeBIDS</span><span class="p">,</span> <span class="n" style="color: #333;">isOnlyBIDS</span><span class="p">,</span> <span class="n" style="color: #333;">isCreateText</span><span class="p">,</span> <span class="n" style="color: #333;">isForceOnsetTimes</span><span class="p">,</span><span class="n" style="color: #333;">isIgnoreDerivedAnd2D</span><span class="p">,</span> <span class="n" style="color: #333;">isPhilipsFloatNotDisplayScaling</span><span class="p">,</span> <span class="n" style="color: #333;">isTiltCorrect</span><span class="p">,</span> <span class="n" style="color: #333;">isRGBplanar</span><span class="p">,</span> <span class="n" style="color: #333;">isOnlySingleFile</span><span class="p">,</span> <span class="n" style="color: #333;">isForceStackDCE</span><span class="p">,</span> <span class="n" style="color: #333;">isRotate3DAcq</span><span class="p">,</span> <span class="n" style="color: #333;">isCrop</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isTestx0021x105E</span><span class="p">,</span> <span class="n" style="color: #333;">isAddNamePostFixes</span><span class="p">,</span> <span class="n" style="color: #333;">isSaveNativeEndian</span><span class="p">,</span> <span class="n" style="color: #333;">isSaveNRRD</span><span class="p">,</span> <span class="n" style="color: #333;">isOneDirAtATime</span><span class="p">,</span> <span class="n" style="color: #333;">isRenameNotConvert</span><span class="p">,</span> <span class="n" style="color: #333;">isSave3D</span><span class="p">,</span> <span class="n" style="color: #333;">isGz</span><span class="p">,</span> <span class="n" style="color: #333;">isPipedGz</span><span class="p">,</span> <span class="n" style="color: #333;">isFlipY</span><span class="p">,</span> <span class="n" style="color: #333;">isCreateBIDS</span><span class="p">,</span> <span class="n" style="color: #333;">isSortDTIbyBVal</span><span class="p">,</span> <span class="n" style="color: #333;">isAnonymizeBIDS</span><span class="p">,</span> <span class="n" style="color: #333;">isOnlyBIDS</span><span class="p">,</span> <span class="n" style="color: #333;">isCreateText</span><span class="p">,</span> <span class="n" style="color: #333;">isForceOnsetTimes</span><span class="p">,</span><span class="n" style="color: #333;">isIgnoreDerivedAnd2D</span><span class="p">,</span> <span class="n" style="color: #333;">isPhilipsFloatNotDisplayScaling</span><span class="p">,</span> <span class="n" style="color: #333;">isTiltCorrect</span><span class="p">,</span> <span class="n" style="color: #333;">isRGBplanar</span><span class="p">,</span> <span class="n" style="color: #333;">isOnlySingleFile</span><span class="p">,</span> <span class="n" style="color: #333;">isForceStackDCE</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">isIgnoreSeriesInstanceUID</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">isRotate3DAcq</span><span class="p">,</span> <span class="n" style="color: #333;">isCrop</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isMaximize16BitRange</span><span class="p">,</span> <span class="n" style="color: #333;">isForceStackSameSeries</span><span class="p">,</span> <span class="n" style="color: #333;">nameConflictBehavior</span><span class="p">,</span> <span class="n" style="color: #333;">isVerbose</span><span class="p">,</span> <span class="n" style="color: #333;">isProgress</span><span class="p">,</span> <span class="n" style="color: #333;">compressFlag</span><span class="p">,</span> <span class="n" style="color: #333;">dirSearchDepth</span><span class="p">,</span> <span class="n" style="color: #333;">gzLevel</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//support for compressed data 0=none,</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[</span><span class="mi" style="color: #099;">512</span><span class="p">],</span> <span class="n" style="color: #333;">outdir</span><span class="p">[</span><span class="mi" style="color: #099;">512</span><span class="p">],</span> <span class="n" style="color: #333;">indir</span><span class="p">[</span><span class="mi" style="color: #099;">512</span><span class="p">],</span> <span class="n" style="color: #333;">pigzname</span><span class="p">[</span><span class="mi" style="color: #099;">512</span><span class="p">],</span> <span class="n" style="color: #333;">optsname</span><span class="p">[</span><span class="mi" style="color: #099;">512</span><span class="p">],</span> <span class="n" style="color: #333;">indirParent</span><span class="p">[</span><span class="mi" style="color: #099;">512</span><span class="p">],</span> <span class="n" style="color: #333;">imageComments</span><span class="p">[</span><span class="mi" style="color: #099;">24</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">seriesNumber</span><span class="p">[</span><span class="n" style="color: #333;">MAX_NUM_SERIES</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">//requires double must store -1 (report but do not convert) as well as seriesUidCrc (uint32)</span></span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#0a3b4127ba41d22e960c99a11ee34694df076301"><strong>console/notarize.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#com.${COMPANY_NAME}.${APP_NAME} e.g. com.mricro.niimath</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">COMPANY_NAME</span><span class="o" style="font-weight: 600;">=</span>mycompany</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">APP_NAME</span><span class="o" style="font-weight: 600;">=</span>dcm2niix</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">APP_SPECIFIC_PASSWORD</span><span class="o" style="font-weight: 600;">=</span>abcd-efgh-ijkl-mnop</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">APPLE_ID_USER</span><span class="o" style="font-weight: 600;">=</span>myname@gmail.com</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">APPLE_ID_INSTALL</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Developer ID Installer: My Name"</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nv" style="color: #008080;">APPLE_ID_APP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Developer ID Application: My Name"</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$APPLE_ID_USER</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"myname@gmail.com"</span> <span class="o" style="font-weight: 600;">]]</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"You need to set your personal IDs and password"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">g++ <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-sectcreate</span> __TEXT __info_plist Info.plist <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp <span class="nt" style="color: #000080;">-o</span> dcm2niixX86 <span class="nt" style="color: #000080;">-DmyDisableOpenJPEG</span> <span class="nt" style="color: #000080;">-target</span> x86_64-apple-macos10.12 <span class="nt" style="color: #000080;">-mmacosx-version-min</span><span class="o" style="font-weight: 600;">=</span>10.12</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">g++ <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-sectcreate</span> __TEXT __info_plist Info.plist <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp <span class="nt" style="color: #000080;">-o</span> dcm2niixARM <span class="nt" style="color: #000080;">-DmyDisableOpenJPEG</span> <span class="nt" style="color: #000080;">-target</span> arm64-apple-macos11 <span class="nt" style="color: #000080;">-mmacosx-version-min</span><span class="o" style="font-weight: 600;">=</span>11.0</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Create the universal binary.</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">strip ./dcm2niixARM<span class="p">;</span> strip ./dcm2niixX86</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">lipo <span class="nt" style="color: #000080;">-create</span> <span class="nt" style="color: #000080;">-output</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span> dcm2niixARM dcm2niixX86</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> ./dcm2niixARM<span class="p">;</span> <span class="nb" style="color: #0086b3;">rm</span> ./dcm2niixX86</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Create a staging area for the installer package.</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> usr/local/bin</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Move the binary into the staging area.</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span> usr/local/bin</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Sign the binary.</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">codesign <span class="nt" style="color: #000080;">--timestamp</span> <span class="nt" style="color: #000080;">--options</span><span class="o" style="font-weight: 600;">=</span>runtime <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APPLE_ID_APP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-v</span> usr/local/bin/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Build the package.</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">pkgbuild <span class="nt" style="color: #000080;">--identifier</span> <span class="s2" style="color: #d14;">"com.</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">COMPANY_NAME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.pkg"</span> <span class="nt" style="color: #000080;">--sign</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APPLE_ID_INSTALL</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--timestamp</span> <span class="nt" style="color: #000080;">--root</span> usr/local <span class="nt" style="color: #000080;">--install-location</span> /usr/local/ <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span>.pkg</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Submit the package to the notarization service.</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">xcrun altool <span class="nt" style="color: #000080;">--notarize-app</span> <span class="nt" style="color: #000080;">--primary-bundle-id</span> <span class="s2" style="color: #d14;">"com.</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">COMPANY_NAME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.pkg"</span> <span class="nt" style="color: #000080;">--username</span> <span class="nv" style="color: #008080;">$APPLE_ID_USER</span> <span class="nt" style="color: #000080;">--password</span> <span class="nv" style="color: #008080;">$APP_SPECIFIC_PASSWORD</span> <span class="nt" style="color: #000080;">--file</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span>.pkg <span class="nt" style="color: #000080;">--output-format</span> xml <span class="o" style="font-weight: 600;">></span> upload_log_file.txt</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># now we need to query apple's server to the status of notarization</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># when the "xcrun altool --notarize-app" command is finished the output plist</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># will contain a notarization-upload->RequestUUID key which we can use to check status</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Checking status..."</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sleep </span>50</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nv" style="color: #008080;">REQUEST_UUID</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>/usr/libexec/PlistBuddy <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;">"Print :notarization-upload:RequestUUID"</span> upload_log_file.txt<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>xcrun altool <span class="nt" style="color: #000080;">--notarization-info</span> <span class="nv" style="color: #008080;">$REQUEST_UUID</span> <span class="nt" style="color: #000080;">-u</span> <span class="nv" style="color: #008080;">$APPLE_ID_USER</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$APP_SPECIFIC_PASSWORD</span> <span class="nt" style="color: #000080;">--output-format</span> xml <span class="o" style="font-weight: 600;">></span> request_log_file.txt</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># parse the request plist for the notarization-info->Status Code key which will</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># be set to "success" if the package was notarized</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"> <span class="nv" style="color: #008080;">STATUS</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>/usr/libexec/PlistBuddy <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;">"Print :notarization-info:Status"</span> request_log_file.txt<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$STATUS</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"in progress"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">break</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo $STATUS</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$STATUS</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sleep </span>10</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># download the log file to view any issues</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell">/usr/bin/curl <span class="nt" style="color: #000080;">-o</span> log_file.txt <span class="sb" style="color: #d14;">`</span>/usr/libexec/PlistBuddy <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;">"Print :notarization-info:LogFileURL"</span> request_log_file.txt<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># staple</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Stapling..."</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell">xcrun stapler staple <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span>.pkg</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell">xcrun stapler validate <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">APP_NAME</span><span class="k" style="font-weight: 600;">}</span>.pkg</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell">open log_file.txt</span></pre>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">dcm2niix (1.0.20210317-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Sat, 24 Apr 2021 14:11:44 +0530</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">dcm2niix (1.0.20201102-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/dcm2niix/-/compare/39040d99618ce400cc521b22884b75a2ea2ddcea...06e79733408f004fd9d7554feaf4d8049c5d7158#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,7 @@ Build-Depends: cmake,</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-sphinx,</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> zlib1g-dev</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/dcm2niix</span>
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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/dcm2niix.git</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: https://github.com/rordenlab/dcm2niix</span>
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