[med-svn] [Git][med-team/mrtrix3][master] 10 commits: d/watch: version=5

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / mrtrix3


Commits:
9523066a by Andreas Tille at 2025-12-17T12:10:37+01:00
d/watch: version=5

- - - - -
5e229d86 by Andreas Tille at 2025-12-17T12:11:00+01:00
New upstream version

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181382a1 by Andreas Tille at 2025-12-17T12:13:51+01:00
New upstream version 3.0.8
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85788a95 by Andreas Tille at 2025-12-17T12:14:01+01:00
Update upstream source from tag 'upstream/3.0.8'

Update to upstream version '3.0.8'
with Debian dir 0d4a4dda7630a85e080762204872f4d8500a9c36
- - - - -
1c908771 by Andreas Tille at 2025-12-17T12:14:31+01:00
Refresh patches

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032ad7de by Andreas Tille at 2025-12-17T12:15:12+01:00
Close bug

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cb7f4d5e by Andreas Tille at 2025-12-17T12:16:27+01:00
Standards-Version: 4.7.2 (routine-update)

- - - - -
00934acb by Andreas Tille at 2025-12-17T12:16:31+01:00
Replace transitional package pkg-config by pkgconf in Build-Depends (routine-update)

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c97bc770 by Andreas Tille at 2025-12-17T13:05:15+01:00
d/copyright: review

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b4c7014a by Andreas Tille at 2025-12-17T13:07:39+01:00
There are no test data provided in /usr/share/doc/mrtrix3 - thus do the test right in the packaging dir

- - - - -


1074 changed files:

- + .git-blame-ignore-revs
- .github/workflows/checks.yml
- .github/workflows/package-linux-anaconda.yml
- .github/workflows/package-macos-anaconda.yml
- .github/workflows/package-macos-native.yml
- .github/workflows/package-windows-msys2.yml
- + .github/workflows/releases.yml
- + .github/workflows/weekly_sanitizers.yml
- .readthedocs.yml
- Dockerfile
- Singularity
- bin/5ttgen
- bin/blend
- bin/convert_bruker
- bin/dwi2response
- bin/dwibiascorrect
- bin/dwicat
- bin/dwifslpreproc
- bin/dwigradcheck
- bin/dwinormalise
- bin/dwishellmath
- bin/for_each
- bin/gen_scheme
- bin/labelsgmfix
- bin/mrtrix3.py
- bin/mrtrix_cleanup
- bin/notfound
- bin/population_template
- bin/responsemean
- build
- check_syntax
- cmd/5tt2gmwmi.cpp
- cmd/5tt2vis.cpp
- cmd/5ttcheck.cpp
- cmd/5ttedit.cpp
- cmd/afdconnectivity.cpp
- cmd/amp2response.cpp
- cmd/amp2sh.cpp
- cmd/connectome2tck.cpp
- cmd/connectomeedit.cpp
- cmd/connectomestats.cpp
- cmd/dcmedit.cpp
- cmd/dcminfo.cpp
- cmd/dirflip.cpp
- cmd/dirgen.cpp
- cmd/dirmerge.cpp
- cmd/dirorder.cpp
- cmd/dirsplit.cpp
- cmd/dirstat.cpp
- cmd/dwi2adc.cpp
- cmd/dwi2fod.cpp
- cmd/dwi2mask.cpp
- cmd/dwi2tensor.cpp
- cmd/dwidenoise.cpp
- cmd/dwiextract.cpp
- cmd/fixel2peaks.cpp
- cmd/fixel2sh.cpp
- cmd/fixel2tsf.cpp
- cmd/fixel2voxel.cpp
- cmd/fixelcfestats.cpp
- cmd/fixelconnectivity.cpp
- cmd/fixelconvert.cpp
- cmd/fixelcorrespondence.cpp
- cmd/fixelcrop.cpp
- cmd/fixelfilter.cpp
- cmd/fixelreorient.cpp
- cmd/fod2dec.cpp
- cmd/fod2fixel.cpp
- cmd/label2colour.cpp
- cmd/label2mesh.cpp
- cmd/labelconvert.cpp
- cmd/labelstats.cpp
- cmd/maskdump.cpp
- cmd/maskfilter.cpp
- cmd/mesh2voxel.cpp
- cmd/meshconvert.cpp
- cmd/meshfilter.cpp
- cmd/mraverageheader.cpp
- cmd/mrcalc.cpp
- cmd/mrcat.cpp
- cmd/mrcentroid.cpp
- cmd/mrcheckerboardmask.cpp
- cmd/mrclusterstats.cpp
- cmd/mrcolour.cpp
- cmd/mrconvert.cpp
- cmd/mrdegibbs.cpp
- cmd/mrdump.cpp
- cmd/mredit.cpp
- cmd/mrfilter.cpp
- cmd/mrgrid.cpp
- cmd/mrhistmatch.cpp
- cmd/mrhistogram.cpp
- cmd/mrinfo.cpp
- cmd/mrmath.cpp
- cmd/mrmetric.cpp
- cmd/mrregister.cpp
- cmd/mrstats.cpp
- cmd/mrthreshold.cpp
- cmd/mrtransform.cpp
- cmd/mrview.cpp
- cmd/mtnormalise.cpp
- cmd/peaks2amp.cpp
- cmd/peaks2fixel.cpp
- cmd/sh2amp.cpp
- cmd/sh2peaks.cpp
- cmd/sh2power.cpp
- cmd/sh2response.cpp
- cmd/shbasis.cpp
- cmd/shconv.cpp
- cmd/shview.cpp
- cmd/tck2connectome.cpp
- cmd/tck2fixel.cpp
- cmd/tckconvert.cpp
- cmd/tckdfc.cpp
- cmd/tckedit.cpp
- cmd/tckgen.cpp
- cmd/tckglobal.cpp
- cmd/tckinfo.cpp
- cmd/tckmap.cpp
- cmd/tckresample.cpp
- cmd/tcksample.cpp
- cmd/tcksift.cpp
- cmd/tcksift2.cpp
- cmd/tckstats.cpp
- cmd/tcktransform.cpp
- cmd/tensor2metric.cpp
- cmd/transformcalc.cpp
- cmd/transformcompose.cpp
- cmd/transformconvert.cpp
- cmd/tsfdivide.cpp
- cmd/tsfinfo.cpp
- cmd/tsfmult.cpp
- cmd/tsfsmooth.cpp
- cmd/tsfthreshold.cpp
- cmd/tsfvalidate.cpp
- cmd/vectorstats.cpp
- cmd/voxel2fixel.cpp
- cmd/voxel2mesh.cpp
- cmd/warp2metric.cpp
- cmd/warpconvert.cpp
- cmd/warpcorrect.cpp
- cmd/warpinit.cpp
- cmd/warpinvert.cpp
- configure
- core/adapter/base.h
- core/adapter/extract.h
- core/adapter/gaussian1D.h
- core/adapter/gradient1D.h
- core/adapter/gradient3D.h
- core/adapter/jacobian.h
- core/adapter/median.h
- core/adapter/neighbourhood3D.h
- core/adapter/normalise3D.h
- core/adapter/permute_axes.h
- core/adapter/regrid.h
- core/adapter/replicate.h
- core/adapter/reslice.cpp
- core/adapter/reslice.h
- core/adapter/subset.h
- core/adapter/warp.h
- core/algo/copy.h
- core/algo/histogram.cpp
- core/algo/histogram.h
- core/algo/iterator.h
- core/algo/loop.h
- core/algo/min_max.h
- core/algo/neighbourhooditerator.h
- core/algo/random_loop.h
- core/algo/random_threaded_loop.h
- core/algo/stochastic_threaded_loop.h
- core/algo/threaded_copy.h
- core/algo/threaded_loop.h
- core/app.cpp
- core/app.h
- core/apply.h
- core/axes.cpp
- core/axes.h
- core/cmdline_option.h
- core/command.h
- core/datatype.cpp
- core/datatype.h
- core/debug.h
- core/dwi/gradient.cpp
- core/dwi/gradient.h
- core/dwi/shells.cpp
- core/dwi/shells.h
- core/eigen_plugins/array.h
- core/eigen_plugins/dense_base.h
- core/eigen_plugins/matrix.h
- core/exception.cpp
- core/exception.h
- core/file/config.cpp
- core/file/config.h
- core/file/copy.h
- core/file/dicom/csa_entry.h
- core/file/dicom/definitions.h
- core/file/dicom/dict.cpp
- core/file/dicom/element.cpp
- core/file/dicom/element.h
- core/file/dicom/image.cpp
- core/file/dicom/image.h
- core/file/dicom/mapper.cpp
- core/file/dicom/mapper.h
- core/file/dicom/patient.cpp
- core/file/dicom/patient.h
- core/file/dicom/quick_scan.cpp
- core/file/dicom/quick_scan.h
- core/file/dicom/select_cmdline.cpp
- core/file/dicom/series.cpp
- core/file/dicom/series.h
- core/file/dicom/study.cpp
- core/file/dicom/study.h
- core/file/dicom/tree.cpp
- core/file/dicom/tree.h
- core/file/entry.h
- core/file/gz.h
- core/file/json_utils.cpp
- core/file/json_utils.h
- core/file/key_value.cpp
- core/file/key_value.h
- core/file/mgh.cpp
- core/file/mgh.h
- core/file/mmap.cpp
- core/file/mmap.h
- core/file/name_parser.cpp
- core/file/name_parser.h
- core/file/nifti2.h
- core/file/nifti_utils.cpp
- core/file/nifti_utils.h
- core/file/ofstream.cpp
- core/file/ofstream.h
- core/file/path.h
- core/file/png.cpp
- core/file/png.h
- core/file/tiff.cpp
- core/file/tiff.h
- core/file/utils.h
- core/filter/base.h
- core/filter/connected_components.cpp
- core/filter/connected_components.h
- core/filter/dilate.h
- core/filter/dwi_brain_mask.h
- core/filter/erode.h
- core/filter/fft.h
- core/filter/gradient.h
- core/filter/mask_clean.h
- core/filter/median.h
- core/filter/normalise.h
- core/filter/optimal_threshold.h
- core/filter/resize.h
- core/filter/reslice.h
- core/filter/smooth.h
- core/filter/warp.h
- core/filter/zclean.h
- core/fixel/helpers.h
- core/fixel/keys.h
- core/fixel/legacy/fixel_metric.h
- core/fixel/legacy/image.h
- core/fixel/legacy/keys.h
- core/fixel/loop.h
- core/fixel/types.h
- core/formats/dicom.cpp
- core/formats/list.cpp
- core/formats/list.h
- core/formats/mgh.cpp
- core/formats/mgz.cpp
- core/formats/mri.cpp
- core/formats/mrtrix.cpp
- core/formats/mrtrix_gz.cpp
- core/formats/mrtrix_sparse_legacy.cpp
- core/formats/mrtrix_utils.cpp
- core/formats/mrtrix_utils.h
- core/formats/nifti1.cpp
- core/formats/nifti1_gz.cpp
- core/formats/nifti2.cpp
- core/formats/nifti2_gz.cpp
- core/formats/par.cpp
- core/formats/pipe.cpp
- core/formats/png.cpp
- core/formats/ram.cpp
- core/formats/tiff.cpp
- core/formats/xds.cpp
- core/header.cpp
- core/header.h
- core/image.h
- core/image_diff.h
- core/image_helpers.h
- core/image_io/base.cpp
- core/image_io/base.h
- core/image_io/default.cpp
- core/image_io/default.h
- core/image_io/fetch_store.cpp
- core/image_io/fetch_store.h
- core/image_io/gz.cpp
- core/image_io/gz.h
- core/image_io/mosaic.cpp
- core/image_io/mosaic.h
- + core/image_io/null.cpp
- + core/image_io/null.h
- core/image_io/pipe.cpp
- core/image_io/pipe.h
- core/image_io/png.cpp
- core/image_io/png.h
- core/image_io/ram.cpp
- core/image_io/ram.h
- core/image_io/scratch.cpp
- core/image_io/scratch.h
- core/image_io/sparse.cpp
- core/image_io/sparse.h
- core/image_io/tiff.cpp
- core/image_io/tiff.h
- core/image_io/variable_scaling.cpp
- core/image_io/variable_scaling.h
- core/interp/base.h
- core/interp/cubic.h
- core/interp/linear.h
- core/interp/masked.h
- core/interp/nearest.h
- core/interp/sinc.h
- core/math/SH.cpp
- core/math/SH.h
- core/math/Sn_scale_estimator.h
- core/math/ZSH.h
- core/math/average_space.cpp
- core/math/average_space.h
- core/math/bessel.cpp
- core/math/bessel.h
- core/math/betainc.cpp
- core/math/betainc.h
- core/math/cauchy.h
- core/math/chebyshev.h
- core/math/check_gradient.h
- core/math/condition_number.h
- core/math/constrained_least_squares.h
- core/math/cubic_spline.h
- core/math/erfinv.cpp
- core/math/erfinv.h
- core/math/factorial.h
- core/math/gaussian.h
- core/math/golden_section_search.h
- core/math/gradient_descent.h
- core/math/gradient_descent_bb.h
- core/math/hermite.h
- core/math/least_squares.h
- core/math/legendre.h
- core/math/math.h
- core/math/median.h
- core/math/polynomial.h
- core/math/quadratic_line_search.h
- core/math/rician.h
- core/math/rng.h
- core/math/sech.h
- core/math/sinc.h
- core/math/sphere.h
- core/math/stats/fwe.cpp
- core/math/stats/fwe.h
- core/math/stats/glm.cpp
- core/math/stats/glm.h
- core/math/stats/import.cpp
- core/math/stats/import.h
- core/math/stats/shuffle.cpp
- core/math/stats/shuffle.h
- core/math/stats/typedefs.h
- core/math/welch_satterthwaite.h
- core/math/zstatistic.cpp
- core/math/zstatistic.h
- core/memory.h
- + core/metadata/bids.cpp
- src/gui/mrview/colourmap_menu.cpp → core/metadata/bids.h
- + core/metadata/phase_encoding.cpp
- + core/metadata/phase_encoding.h
- + core/metadata/slice_encoding.cpp
- src/gui/mrview/colourmap_menu.h → core/metadata/slice_encoding.h
- core/misc/bitset.cpp
- core/misc/bitset.h
- core/misc/voxel2vector.h
- core/mrtrix.cpp
- core/mrtrix.h
- core/ordered_thread_queue.h
- − core/phase_encoding.cpp
- − core/phase_encoding.h
- core/progressbar.cpp
- core/progressbar.h
- core/raw.h
- core/signal_handler.cpp
- core/signal_handler.h
- core/signals.h
- + core/spinlock.h
- core/stats.cpp
- core/stats.h
- core/stride.cpp
- core/stride.h
- core/thread.cpp
- core/thread.h
- core/thread_queue.h
- core/timer.h
- core/transform.h
- core/types.h
- core/version.h
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/mrtrix_version.patch
- debian/patches/python3.patch
- debian/tests/run-unit-test
- debian/watch
- docs/Makefile
- + docs/concepts/mrview_lock_axes/lockoff_nointerp.gif
- + docs/concepts/mrview_lock_axes/lockoff_withinterp.gif
- + docs/concepts/mrview_lock_axes/lockon_nohighlight.gif
- + docs/concepts/mrview_lock_axes/lockon_withhighlight.gif
- + docs/concepts/mrview_lock_axes/mrview_lock_axes.rst
- + docs/concepts/mrview_lock_axes/overlay.png
- docs/concepts/pe_scheme.rst
- docs/conf.py
- docs/constrained_spherical_deconvolution/multi_shell_multi_tissue_csd.rst
- docs/constrained_spherical_deconvolution/response_function_estimation.rst
- docs/format_config_options
- docs/format_environment_variables
- docs/generate_user_docs.sh
- docs/index.rst
- docs/installation/using_containers.rst
- docs/make.bat
- docs/reference/commands/5tt2gmwmi.rst
- docs/reference/commands/5tt2vis.rst
- docs/reference/commands/5ttcheck.rst
- docs/reference/commands/5ttedit.rst
- docs/reference/commands/5ttgen.rst
- docs/reference/commands/afdconnectivity.rst
- docs/reference/commands/amp2response.rst
- docs/reference/commands/amp2sh.rst
- docs/reference/commands/connectome2tck.rst
- docs/reference/commands/connectomeedit.rst
- docs/reference/commands/connectomestats.rst
- docs/reference/commands/dcmedit.rst
- docs/reference/commands/dcminfo.rst
- docs/reference/commands/dirflip.rst
- docs/reference/commands/dirgen.rst
- docs/reference/commands/dirmerge.rst
- docs/reference/commands/dirorder.rst
- docs/reference/commands/dirsplit.rst
- docs/reference/commands/dirstat.rst
- docs/reference/commands/dwi2adc.rst
- docs/reference/commands/dwi2fod.rst
- docs/reference/commands/dwi2mask.rst
- docs/reference/commands/dwi2response.rst
- docs/reference/commands/dwi2tensor.rst
- docs/reference/commands/dwibiascorrect.rst
- docs/reference/commands/dwicat.rst
- docs/reference/commands/dwiextract.rst
- docs/reference/commands/dwifslpreproc.rst
- docs/reference/commands/dwigradcheck.rst
- docs/reference/commands/dwinormalise.rst
- docs/reference/commands/dwishellmath.rst
- docs/reference/commands/fixel2peaks.rst
- docs/reference/commands/fixel2sh.rst
- docs/reference/commands/fixel2tsf.rst
- docs/reference/commands/fixel2voxel.rst
- docs/reference/commands/fixelcfestats.rst
- docs/reference/commands/fixelconnectivity.rst
- docs/reference/commands/fixelconvert.rst
- docs/reference/commands/fixelcorrespondence.rst
- docs/reference/commands/fixelcrop.rst
- docs/reference/commands/fixelfilter.rst
- docs/reference/commands/fixelreorient.rst
- docs/reference/commands/fod2fixel.rst
- docs/reference/commands/for_each.rst
- docs/reference/commands/label2colour.rst
- docs/reference/commands/label2mesh.rst
- docs/reference/commands/labelconvert.rst
- docs/reference/commands/labelsgmfix.rst
- docs/reference/commands/labelstats.rst
- docs/reference/commands/maskdump.rst
- docs/reference/commands/maskfilter.rst
- docs/reference/commands/mesh2voxel.rst
- docs/reference/commands/meshconvert.rst
- docs/reference/commands/meshfilter.rst
- docs/reference/commands/mraverageheader.rst
- docs/reference/commands/mrcalc.rst
- docs/reference/commands/mrcat.rst
- docs/reference/commands/mrcentroid.rst
- docs/reference/commands/mrcheckerboardmask.rst
- docs/reference/commands/mrclusterstats.rst
- docs/reference/commands/mrcolour.rst
- docs/reference/commands/mrconvert.rst
- docs/reference/commands/mrdegibbs.rst
- docs/reference/commands/mrdump.rst
- docs/reference/commands/mredit.rst
- docs/reference/commands/mrfilter.rst
- docs/reference/commands/mrgrid.rst
- docs/reference/commands/mrhistmatch.rst
- docs/reference/commands/mrhistogram.rst
- docs/reference/commands/mrinfo.rst
- docs/reference/commands/mrmath.rst
- docs/reference/commands/mrmetric.rst
- docs/reference/commands/mrregister.rst
- docs/reference/commands/mrstats.rst
- docs/reference/commands/mrthreshold.rst
- docs/reference/commands/mrtransform.rst
- docs/reference/commands/mrtrix_cleanup.rst
- docs/reference/commands/mrview.rst
- docs/reference/commands/mtnormalise.rst
- docs/reference/commands/peaks2amp.rst
- docs/reference/commands/peaks2fixel.rst
- docs/reference/commands/population_template.rst
- docs/reference/commands/responsemean.rst
- docs/reference/commands/sh2amp.rst
- docs/reference/commands/sh2peaks.rst
- docs/reference/commands/sh2power.rst
- docs/reference/commands/sh2response.rst
- docs/reference/commands/shbasis.rst
- docs/reference/commands/shconv.rst
- docs/reference/commands/shview.rst
- docs/reference/commands/tck2connectome.rst
- docs/reference/commands/tck2fixel.rst
- docs/reference/commands/tckconvert.rst
- docs/reference/commands/tckdfc.rst
- docs/reference/commands/tckedit.rst
- docs/reference/commands/tckgen.rst
- docs/reference/commands/tckinfo.rst
- docs/reference/commands/tckmap.rst
- docs/reference/commands/tckresample.rst
- docs/reference/commands/tcksample.rst
- docs/reference/commands/tcksift.rst
- docs/reference/commands/tcksift2.rst
- docs/reference/commands/tckstats.rst
- docs/reference/commands/tcktransform.rst
- docs/reference/commands/tensor2metric.rst
- docs/reference/commands/transformcalc.rst
- docs/reference/commands/transformcompose.rst
- docs/reference/commands/transformconvert.rst
- docs/reference/commands/tsfdivide.rst
- docs/reference/commands/tsfinfo.rst
- docs/reference/commands/tsfmult.rst
- docs/reference/commands/tsfsmooth.rst
- docs/reference/commands/tsfthreshold.rst
- docs/reference/commands/tsfvalidate.rst
- docs/reference/commands/vectorstats.rst
- docs/reference/commands/voxel2fixel.rst
- docs/reference/commands/voxel2mesh.rst
- docs/reference/commands/warp2metric.rst
- docs/reference/commands/warpconvert.rst
- docs/reference/commands/warpcorrect.rst
- docs/reference/commands/warpinit.rst
- docs/reference/commands/warpinvert.rst
- docs/requirements.txt
- docs/tips_and_tricks/dicom_handling.rst
- doxygen
- generate_bash_completion.py
- install_mime_types.sh
- lib/mrtrix3/_5ttgen/freesurfer.py
- lib/mrtrix3/_5ttgen/fsl.py
- lib/mrtrix3/_5ttgen/gif.py
- lib/mrtrix3/_5ttgen/hsvs.py
- lib/mrtrix3/__init__.py
- lib/mrtrix3/algorithm.py
- lib/mrtrix3/app.py
- lib/mrtrix3/dwi2response/dhollander.py
- lib/mrtrix3/dwi2response/fa.py
- lib/mrtrix3/dwi2response/manual.py
- lib/mrtrix3/dwi2response/msmt_5tt.py
- lib/mrtrix3/dwi2response/tax.py
- lib/mrtrix3/dwi2response/tournier.py
- lib/mrtrix3/dwibiascorrect/ants.py
- lib/mrtrix3/dwibiascorrect/fsl.py
- lib/mrtrix3/dwinormalise/group.py
- lib/mrtrix3/dwinormalise/individual.py
- lib/mrtrix3/fsl.py
- lib/mrtrix3/image.py
- lib/mrtrix3/matrix.py
- lib/mrtrix3/path.py
- lib/mrtrix3/phaseencoding.py
- lib/mrtrix3/run.py
- lib/mrtrix3/sh.py
- lib/mrtrix3/utils.py
- matlab/private/add_field.m
- matlab/read_mrtrix.m
- matlab/read_mrtrix_tracks.m
- matlab/read_mrtrix_tsf.m
- matlab/write_mrtrix.m
- matlab/write_mrtrix_tracks.m
- matlab/write_mrtrix_tsf.m
- mrview.desktop
- package_mrtrix
- run_pylint
- run_tests
- set_path
- share/mrtrix3/_5ttgen/FreeSurfer2ACT.txt
- share/mrtrix3/_5ttgen/FreeSurfer2ACT_sgm_amyg_hipp.txt
- share/mrtrix3/_5ttgen/hsvs/AmygSubfields.txt
- share/mrtrix3/_5ttgen/hsvs/HippSubfields.txt
- share/mrtrix3/labelconvert/aal.txt
- share/mrtrix3/labelconvert/aal2.txt
- share/mrtrix3/labelconvert/fs2lobes_cinginc_convert.txt
- share/mrtrix3/labelconvert/fs2lobes_cinginc_labels.txt
- share/mrtrix3/labelconvert/fs2lobes_cingsep_convert.txt
- share/mrtrix3/labelconvert/fs2lobes_cingsep_labels.txt
- share/mrtrix3/labelconvert/fs_a2009s.txt
- share/mrtrix3/labelconvert/fs_default.txt
- share/mrtrix3/labelconvert/hcpmmp1_ordered.txt
- share/mrtrix3/labelconvert/hcpmmp1_original.txt
- share/mrtrix3/labelconvert/lpba40.txt
- share/mrtrix3/labelsgmfix/FreeSurferSGM.txt
- src/colourmap.cpp
- src/colourmap.h
- src/connectome/connectome.cpp
- src/connectome/connectome.h
- src/connectome/enhance.cpp
- src/connectome/enhance.h
- src/connectome/lut.cpp
- src/connectome/lut.h
- src/connectome/mat2vec.h
- src/dwi/bootstrap.h
- src/dwi/directions/file.cpp
- src/dwi/directions/file.h
- src/dwi/directions/mask.cpp
- src/dwi/directions/mask.h
- src/dwi/directions/predefined.cpp
- src/dwi/directions/predefined.h
- src/dwi/directions/set.cpp
- src/dwi/directions/set.h
- src/dwi/fixel_map.h
- src/dwi/fmls.cpp
- src/dwi/fmls.h
- src/dwi/noise_estimator.h
- src/dwi/sdeconv/csd.cpp
- src/dwi/sdeconv/csd.h
- src/dwi/sdeconv/msmt_csd.cpp
- src/dwi/sdeconv/msmt_csd.h
- src/dwi/tensor.h
- src/dwi/tractography/ACT/act.cpp
- src/dwi/tractography/ACT/act.h
- src/dwi/tractography/ACT/gmwmi.cpp
- src/dwi/tractography/ACT/gmwmi.h
- src/dwi/tractography/ACT/method.h
- src/dwi/tractography/ACT/shared.h
- src/dwi/tractography/ACT/tissues.h
- src/dwi/tractography/GT/energy.h
- src/dwi/tractography/GT/externalenergy.cpp
- src/dwi/tractography/GT/externalenergy.h
- src/dwi/tractography/GT/gt.cpp
- src/dwi/tractography/GT/gt.h
- src/dwi/tractography/GT/internalenergy.cpp
- src/dwi/tractography/GT/internalenergy.h
- src/dwi/tractography/GT/mhsampler.cpp
- src/dwi/tractography/GT/mhsampler.h
- src/dwi/tractography/GT/particle.cpp
- src/dwi/tractography/GT/particle.h
- src/dwi/tractography/GT/particlegrid.cpp
- src/dwi/tractography/GT/particlegrid.h
- src/dwi/tractography/GT/particlepool.h
- src/dwi/tractography/GT/spatiallock.h
- src/dwi/tractography/SIFT/fixel.h
- src/dwi/tractography/SIFT/gradient_sort.cpp
- src/dwi/tractography/SIFT/gradient_sort.h
- src/dwi/tractography/SIFT/model.h
- src/dwi/tractography/SIFT/model_base.h
- src/dwi/tractography/SIFT/output.h
- src/dwi/tractography/SIFT/proc_mask.cpp
- src/dwi/tractography/SIFT/proc_mask.h
- src/dwi/tractography/SIFT/sift.cpp
- src/dwi/tractography/SIFT/sift.h
- src/dwi/tractography/SIFT/sifter.cpp
- src/dwi/tractography/SIFT/sifter.h
- src/dwi/tractography/SIFT/track_contribution.cpp
- src/dwi/tractography/SIFT/track_contribution.h
- src/dwi/tractography/SIFT/track_index_range.cpp
- src/dwi/tractography/SIFT/track_index_range.h
- src/dwi/tractography/SIFT/types.h
- src/dwi/tractography/SIFT2/coeff_optimiser.cpp
- src/dwi/tractography/SIFT2/coeff_optimiser.h
- src/dwi/tractography/SIFT2/fixel.h
- src/dwi/tractography/SIFT2/fixel_updater.cpp
- src/dwi/tractography/SIFT2/fixel_updater.h
- src/dwi/tractography/SIFT2/line_search.cpp
- src/dwi/tractography/SIFT2/line_search.h
- src/dwi/tractography/SIFT2/reg_calculator.cpp
- src/dwi/tractography/SIFT2/reg_calculator.h
- src/dwi/tractography/SIFT2/regularisation.h
- src/dwi/tractography/SIFT2/streamline_stats.cpp
- src/dwi/tractography/SIFT2/streamline_stats.h
- src/dwi/tractography/SIFT2/tckfactor.cpp
- src/dwi/tractography/SIFT2/tckfactor.h
- src/dwi/tractography/algorithms/calibrator.h
- src/dwi/tractography/algorithms/fact.h
- src/dwi/tractography/algorithms/iFOD1.cpp
- src/dwi/tractography/algorithms/iFOD1.h
- src/dwi/tractography/algorithms/iFOD2.cpp
- src/dwi/tractography/algorithms/iFOD2.h
- src/dwi/tractography/algorithms/nulldist.h
- src/dwi/tractography/algorithms/sd_stream.h
- src/dwi/tractography/algorithms/seedtest.h
- src/dwi/tractography/algorithms/tensor_det.h
- src/dwi/tractography/algorithms/tensor_prob.h
- src/dwi/tractography/connectome/connectome.cpp
- src/dwi/tractography/connectome/connectome.h
- src/dwi/tractography/connectome/exemplar.cpp
- src/dwi/tractography/connectome/exemplar.h
- src/dwi/tractography/connectome/extract.cpp
- src/dwi/tractography/connectome/extract.h
- src/dwi/tractography/connectome/mapped_track.h
- src/dwi/tractography/connectome/mapper.h
- src/dwi/tractography/connectome/matrix.cpp
- src/dwi/tractography/connectome/matrix.h
- src/dwi/tractography/connectome/metric.h
- src/dwi/tractography/connectome/streamline.h
- src/dwi/tractography/connectome/tck2nodes.cpp
- src/dwi/tractography/connectome/tck2nodes.h
- src/dwi/tractography/editing/editing.cpp
- src/dwi/tractography/editing/editing.h
- src/dwi/tractography/editing/loader.h
- src/dwi/tractography/editing/receiver.cpp
- src/dwi/tractography/editing/receiver.h
- src/dwi/tractography/editing/worker.cpp
- src/dwi/tractography/editing/worker.h
- src/dwi/tractography/file.h
- src/dwi/tractography/file_base.cpp
- src/dwi/tractography/file_base.h
- src/dwi/tractography/mapping/buffer_scratch_dump.h
- src/dwi/tractography/mapping/fixel_td_map.cpp
- src/dwi/tractography/mapping/fixel_td_map.h
- src/dwi/tractography/mapping/gaussian/mapper.cpp
- src/dwi/tractography/mapping/gaussian/mapper.h
- src/dwi/tractography/mapping/gaussian/voxel.h
- src/dwi/tractography/mapping/loader.h
- src/dwi/tractography/mapping/mapper.cpp
- src/dwi/tractography/mapping/mapper.h
- src/dwi/tractography/mapping/mapper_plugins.cpp
- src/dwi/tractography/mapping/mapper_plugins.h
- src/dwi/tractography/mapping/mapping.cpp
- src/dwi/tractography/mapping/mapping.h
- src/dwi/tractography/mapping/twi_stats.cpp
- src/dwi/tractography/mapping/twi_stats.h
- src/dwi/tractography/mapping/voxel.cpp
- src/dwi/tractography/mapping/voxel.h
- src/dwi/tractography/mapping/writer.cpp
- src/dwi/tractography/mapping/writer.h
- src/dwi/tractography/properties.cpp
- src/dwi/tractography/properties.h
- src/dwi/tractography/resampling/arc.cpp
- src/dwi/tractography/resampling/arc.h
- src/dwi/tractography/resampling/downsampler.cpp
- src/dwi/tractography/resampling/downsampler.h
- src/dwi/tractography/resampling/endpoints.cpp
- src/dwi/tractography/resampling/endpoints.h
- src/dwi/tractography/resampling/fixed_num_points.cpp
- src/dwi/tractography/resampling/fixed_num_points.h
- src/dwi/tractography/resampling/fixed_step_size.cpp
- src/dwi/tractography/resampling/fixed_step_size.h
- src/dwi/tractography/resampling/resampling.cpp
- src/dwi/tractography/resampling/resampling.h
- src/dwi/tractography/resampling/upsampler.cpp
- src/dwi/tractography/resampling/upsampler.h
- src/dwi/tractography/rng.cpp
- src/dwi/tractography/rng.h
- src/dwi/tractography/roi.cpp
- src/dwi/tractography/roi.h
- src/dwi/tractography/scalar_file.h
- src/dwi/tractography/seeding/base.h
- src/dwi/tractography/seeding/basic.cpp
- src/dwi/tractography/seeding/basic.h
- src/dwi/tractography/seeding/dynamic.cpp
- src/dwi/tractography/seeding/dynamic.h
- src/dwi/tractography/seeding/gmwmi.cpp
- src/dwi/tractography/seeding/gmwmi.h
- src/dwi/tractography/seeding/list.cpp
- src/dwi/tractography/seeding/list.h
- src/dwi/tractography/seeding/seeding.cpp
- src/dwi/tractography/seeding/seeding.h
- src/dwi/tractography/streamline.h
- src/dwi/tractography/tracking/early_exit.cpp
- src/dwi/tractography/tracking/early_exit.h
- src/dwi/tractography/tracking/exec.h
- src/dwi/tractography/tracking/generated_track.h
- src/dwi/tractography/tracking/method.cpp
- src/dwi/tractography/tracking/method.h
- src/dwi/tractography/tracking/shared.cpp
- src/dwi/tractography/tracking/shared.h
- src/dwi/tractography/tracking/tractography.cpp
- src/dwi/tractography/tracking/tractography.h
- src/dwi/tractography/tracking/types.h
- src/dwi/tractography/tracking/write_kernel.cpp
- src/dwi/tractography/tracking/write_kernel.h
- src/dwi/tractography/weights.cpp
- src/dwi/tractography/weights.h
- src/exec_version.h
- src/fixel/filter/base.h
- src/fixel/filter/connect.cpp
- src/fixel/filter/connect.h
- src/fixel/filter/smooth.cpp
- src/fixel/filter/smooth.h
- src/fixel/index_remapper.cpp
- src/fixel/index_remapper.h
- src/fixel/matrix.cpp
- src/fixel/matrix.h
- src/gui/color_button.cpp
- src/gui/color_button.h
- src/gui/crosshair.cpp
- src/gui/crosshair.h
- src/gui/cursor.cpp
- src/gui/cursor.h
- src/gui/dialog/dialog.cpp
- src/gui/dialog/dialog.h
- src/gui/dialog/dicom.cpp
- src/gui/dialog/dicom.h
- src/gui/dialog/file.cpp
- src/gui/dialog/file.h
- src/gui/dialog/image_properties.cpp
- src/gui/dialog/image_properties.h
- src/gui/dialog/list.cpp
- src/gui/dialog/list.h
- src/gui/dialog/opengl.cpp
- src/gui/dialog/opengl.h
- src/gui/dialog/progress.cpp
- src/gui/dialog/progress.h
- src/gui/dialog/report_exception.cpp
- src/gui/dialog/report_exception.h
- src/gui/dwi/render_frame.cpp
- src/gui/dwi/render_frame.h
- src/gui/dwi/renderer.cpp
- src/gui/dwi/renderer.h
- src/gui/gui.cpp
- src/gui/gui.h
- src/gui/lighting_dock.cpp
- src/gui/lighting_dock.h
- src/gui/mrview/adjust_button.cpp
- src/gui/mrview/adjust_button.h
- src/gui/mrview/colourbars.cpp
- src/gui/mrview/colourbars.h
- src/gui/mrview/colourmap_button.cpp
- src/gui/mrview/colourmap_button.h
- src/gui/mrview/combo_box_error.cpp
- src/gui/mrview/combo_box_error.h
- src/gui/mrview/displayable.cpp
- src/gui/mrview/displayable.h
- src/gui/mrview/file_open.cpp
- src/gui/mrview/file_open.h
- src/gui/mrview/gui_image.cpp
- src/gui/mrview/gui_image.h
- src/gui/mrview/icons.h
- src/gui/mrview/mode/base.cpp
- src/gui/mrview/mode/base.h
- src/gui/mrview/mode/lightbox.cpp
- src/gui/mrview/mode/lightbox.h
- src/gui/mrview/mode/lightbox_gui.h
- src/gui/mrview/mode/list.h
- src/gui/mrview/mode/ortho.cpp
- src/gui/mrview/mode/ortho.h
- src/gui/mrview/mode/slice.cpp
- src/gui/mrview/mode/slice.h
- src/gui/mrview/mode/volume.cpp
- src/gui/mrview/mode/volume.h
- src/gui/mrview/spin_box.h
- src/gui/mrview/sync/client.cpp
- src/gui/mrview/sync/client.h
- src/gui/mrview/sync/enums.h
- src/gui/mrview/sync/interprocesscommunicator.cpp
- src/gui/mrview/sync/interprocesscommunicator.h
- src/gui/mrview/sync/localsocketreader.cpp
- src/gui/mrview/sync/localsocketreader.h
- src/gui/mrview/sync/processlock.cpp
- src/gui/mrview/sync/processlock.h
- src/gui/mrview/sync/syncmanager.cpp
- src/gui/mrview/sync/syncmanager.h
- src/gui/mrview/tool/base.cpp
- src/gui/mrview/tool/base.h
- src/gui/mrview/tool/connectome/colourmap_observers.cpp
- src/gui/mrview/tool/connectome/colourmap_observers.h
- src/gui/mrview/tool/connectome/connectome.cpp
- src/gui/mrview/tool/connectome/connectome.h
- src/gui/mrview/tool/connectome/edge.cpp
- src/gui/mrview/tool/connectome/edge.h
- src/gui/mrview/tool/connectome/file_data_vector.cpp
- src/gui/mrview/tool/connectome/file_data_vector.h
- src/gui/mrview/tool/connectome/matrix_list.cpp
- src/gui/mrview/tool/connectome/matrix_list.h
- src/gui/mrview/tool/connectome/node.cpp
- src/gui/mrview/tool/connectome/node.h
- src/gui/mrview/tool/connectome/node_list.cpp
- src/gui/mrview/tool/connectome/node_list.h
- src/gui/mrview/tool/connectome/node_overlay.cpp
- src/gui/mrview/tool/connectome/node_overlay.h
- src/gui/mrview/tool/connectome/selection.cpp
- src/gui/mrview/tool/connectome/selection.h
- src/gui/mrview/tool/connectome/shaders.cpp
- src/gui/mrview/tool/connectome/shaders.h
- src/gui/mrview/tool/connectome/types.h
- src/gui/mrview/tool/fixel/base_fixel.cpp
- src/gui/mrview/tool/fixel/base_fixel.h
- src/gui/mrview/tool/fixel/directory.cpp
- src/gui/mrview/tool/fixel/directory.h
- src/gui/mrview/tool/fixel/fixel.cpp
- src/gui/mrview/tool/fixel/fixel.h
- src/gui/mrview/tool/fixel/image4D.cpp
- src/gui/mrview/tool/fixel/image4D.h
- src/gui/mrview/tool/fixel/legacy.cpp
- src/gui/mrview/tool/fixel/legacy.h
- src/gui/mrview/tool/fixel/vector_structs.h
- src/gui/mrview/tool/list.h
- src/gui/mrview/tool/list_model_base.h
- src/gui/mrview/tool/odf/item.cpp
- src/gui/mrview/tool/odf/item.h
- src/gui/mrview/tool/odf/model.cpp
- src/gui/mrview/tool/odf/model.h
- src/gui/mrview/tool/odf/odf.cpp
- src/gui/mrview/tool/odf/odf.h
- src/gui/mrview/tool/odf/preview.cpp
- src/gui/mrview/tool/odf/preview.h
- src/gui/mrview/tool/odf/type.h
- src/gui/mrview/tool/overlay.cpp
- src/gui/mrview/tool/overlay.h
- src/gui/mrview/tool/roi_editor/item.cpp
- src/gui/mrview/tool/roi_editor/item.h
- src/gui/mrview/tool/roi_editor/model.cpp
- src/gui/mrview/tool/roi_editor/model.h
- src/gui/mrview/tool/roi_editor/roi.cpp
- src/gui/mrview/tool/roi_editor/roi.h
- src/gui/mrview/tool/roi_editor/undoentry.cpp
- src/gui/mrview/tool/roi_editor/undoentry.h
- src/gui/mrview/tool/screen_capture.cpp
- src/gui/mrview/tool/screen_capture.h
- src/gui/mrview/tool/tractography/track_scalar_file.cpp
- src/gui/mrview/tool/tractography/track_scalar_file.h
- src/gui/mrview/tool/tractography/tractogram.cpp
- src/gui/mrview/tool/tractography/tractogram.h
- src/gui/mrview/tool/tractography/tractogram_enums.h
- src/gui/mrview/tool/tractography/tractography.cpp
- src/gui/mrview/tool/tractography/tractography.h
- src/gui/mrview/tool/transform.cpp
- src/gui/mrview/tool/transform.h
- src/gui/mrview/tool/view.cpp
- src/gui/mrview/tool/view.h
- src/gui/mrview/volume.cpp
- src/gui/mrview/volume.h
- src/gui/mrview/window.cpp
- src/gui/mrview/window.h
- src/gui/opengl/font.cpp
- src/gui/opengl/font.h
- src/gui/opengl/gl.cpp
- src/gui/opengl/gl.h
- src/gui/opengl/gl_core_3_3.cpp
- src/gui/opengl/gl_core_3_3.h
- src/gui/opengl/lighting.cpp
- src/gui/opengl/lighting.h
- src/gui/opengl/shader.cpp
- src/gui/opengl/shader.h
- src/gui/opengl/transformation.h
- src/gui/projection.cpp
- src/gui/projection.h
- src/gui/shapes/cube.cpp
- src/gui/shapes/cube.h
- src/gui/shapes/cylinder.cpp
- src/gui/shapes/cylinder.h
- src/gui/shapes/halfsphere.cpp
- src/gui/shapes/halfsphere.h
- src/gui/shapes/sphere.cpp
- src/gui/shapes/sphere.h
- src/gui/shview/file_open.cpp
- src/gui/shview/file_open.h
- src/gui/shview/icons.h
- src/gui/shview/render_window.cpp
- src/gui/shview/render_window.h
- src/min_mem_array.h
- src/registration/linear.cpp
- src/registration/linear.h
- src/registration/metric/cc_helper.h
- src/registration/metric/cross_correlation.h
- src/registration/metric/demons.h
- src/registration/metric/demons4D.h
- src/registration/metric/demons_cc.h
- src/registration/metric/difference_robust.h
- src/registration/metric/evaluate.h
- src/registration/metric/linear_base.h
- src/registration/metric/local_cross_correlation.h
- src/registration/metric/mean_squared.h
- src/registration/metric/params.h
- src/registration/metric/robust_estimators.h
- src/registration/metric/thread_kernel.h
- src/registration/multi_contrast.cpp
- src/registration/multi_contrast.h
- src/registration/multi_resolution_lmax.h
- src/registration/nonlinear.cpp
- src/registration/nonlinear.h
- src/registration/shared.h
- src/registration/transform/affine.cpp
- src/registration/transform/affine.h
- src/registration/transform/base.h
- src/registration/transform/convergence_check.cpp
- src/registration/transform/convergence_check.h
- src/registration/transform/initialiser.cpp
- src/registration/transform/initialiser.h
- src/registration/transform/initialiser_helpers.cpp
- src/registration/transform/initialiser_helpers.h
- src/registration/transform/reorient.h
- src/registration/transform/rigid.cpp
- src/registration/transform/rigid.h
- src/registration/transform/robust.cpp
- src/registration/transform/search.h
- src/registration/warp/compose.h
- src/registration/warp/convert.h
- src/registration/warp/helpers.h
- src/registration/warp/invert.h
- src/stats/cfe.cpp
- src/stats/cfe.h
- src/stats/cluster.cpp
- src/stats/cluster.h
- src/stats/enhance.h
- src/stats/permstack.cpp
- src/stats/permstack.h
- src/stats/permtest.cpp
- src/stats/permtest.h
- src/stats/tfce.cpp
- src/stats/tfce.h
- src/surface/algo/image2mesh.h
- src/surface/algo/mesh2image.cpp
- src/surface/algo/mesh2image.h
- src/surface/filter/base.cpp
- src/surface/filter/base.h
- src/surface/filter/smooth.cpp
- src/surface/filter/smooth.h
- src/surface/filter/vertex_transform.cpp
- src/surface/filter/vertex_transform.h
- src/surface/freesurfer.cpp
- src/surface/freesurfer.h
- src/surface/mesh.cpp
- src/surface/mesh.h
- src/surface/mesh_multi.cpp
- src/surface/mesh_multi.h
- src/surface/polygon.cpp
- src/surface/polygon.h
- src/surface/scalar.cpp
- src/surface/scalar.h
- src/surface/types.h
- src/surface/utils.h
- src/wrap_r.h
- testing/binaries/tests/dwidenoise
- testing/binaries/tests/fixelcfestats
- testing/binaries/tests/mesh2voxel
- testing/binaries/tests/meshconvert
- testing/binaries/tests/mrcalc
- testing/binaries/tests/mrcat
- testing/binaries/tests/mrcolour
- testing/binaries/tests/mrconvert
- + testing/binaries/tests/mrinfo
- + testing/binaries/tests/tckglobal
- testing/binaries/tests/tckresample
- testing/binaries/tests/vectorstats
- testing/cmd/testing_diff_dir.cpp
- testing/cmd/testing_diff_fixel.cpp
- testing/cmd/testing_diff_fixel_old.cpp
- testing/cmd/testing_diff_header.cpp
- testing/cmd/testing_diff_image.cpp
- testing/cmd/testing_diff_matrix.cpp
- testing/cmd/testing_diff_mesh.cpp
- testing/cmd/testing_diff_peaks.cpp
- testing/cmd/testing_diff_tck.cpp
- testing/cmd/testing_diff_tsf.cpp
- testing/cmd/testing_gen_data.cpp
- testing/cmd/testing_unit_tests_bitset.cpp
- testing/cmd/testing_unit_tests_erfinv.cpp
- testing/cmd/testing_unit_tests_icls.cpp
- testing/cmd/testing_unit_tests_ordered_include.cpp
- testing/cmd/testing_unit_tests_ordered_queue.cpp
- testing/cmd/testing_unit_tests_parse_ints.cpp
- testing/cmd/testing_unit_tests_sh_precomputer.cpp
- testing/cmd/testing_unit_tests_shuffle.cpp
- testing/cmd/testing_unit_tests_to.cpp
- testing/pylint.rc
- testing/scripts/tests/dwifslpreproc
- testing/src/diff_images.h
- testing/src/unit_tests/tractography/roi_unit_tests.h
- testing/src/unit_tests/unit_test.h
- update_copyright
- update_dev_doc


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