[Neurodebian-users] missing some of ANTs' tools
Yaroslav Halchenko
debian at onerussian.com
Wed Dec 5 16:18:25 UTC 2012
thanks for the report!
On Wed, 05 Dec 2012, Christian Stephan-Otto wrote:
> I don't seem to find Atropos nor antsRegistration in my ANTs installation.
1. Atropos Indeed, this one is not present in builds for older
Debian/Ubuntu releases because
IF( ITK_USE_REVIEW_STATISTICS )
ADD_EXECUTABLE(Atropos Atropos.cxx ${UI_SOURCES})
TARGET_LINK_LIBRARIES(Atropos ITKCommon ITKBasicFilters ITKIO ITKStatistics )
ENDIF( ITK_USE_REVIEW_STATISTICS )
i.e. requires ITK build with REVIEW_STATISTICS which was enabled only
recently thus present only on recent Debian/Ubuntus:
~/deb/builds/ants/1.9.2+svn680.dfsg-4$ for f in *deb; do echo $f; dpkg -c $f | grep -e Atropos -e antsRegistration; done
ants_1.9.2+svn680.dfsg-4_amd64.deb
-rwxr-xr-x root/root 4208336 2012-05-04 11:08 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 11:08 ./usr/share/man/man1/Atropos.1.gz
ants_1.9.2+svn680.dfsg-4~nd10.04+1_amd64.deb
ants_1.9.2+svn680.dfsg-4~nd10.04+1_i386.deb
ants_1.9.2+svn680.dfsg-4~nd10.10+1_amd64.deb
ants_1.9.2+svn680.dfsg-4~nd10.10+1_i386.deb
ants_1.9.2+svn680.dfsg-4~nd11.04+1_amd64.deb
ants_1.9.2+svn680.dfsg-4~nd11.04+1_i386.deb
ants_1.9.2+svn680.dfsg-4~nd11.10+1_amd64.deb
-rwxr-xr-x root/root 4142016 2012-05-04 18:23 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 18:23 ./usr/share/man/man1/Atropos.1.gz
ants_1.9.2+svn680.dfsg-4~nd11.10+1_i386.deb
-rwxr-xr-x root/root 3963720 2012-05-04 17:48 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 17:48 ./usr/share/man/man1/Atropos.1.gz
ants_1.9.2+svn680.dfsg-4~nd12.04+1_amd64.deb
-rwxr-xr-x root/root 4146120 2012-05-04 19:29 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 19:28 ./usr/share/man/man1/Atropos.1.gz
ants_1.9.2+svn680.dfsg-4~nd12.04+1_i386.deb
-rwxr-xr-x root/root 3963724 2012-05-04 18:54 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 18:54 ./usr/share/man/man1/Atropos.1.gz
ants_1.9.2+svn680.dfsg-4~nd+1_amd64.deb
-rwxr-xr-x root/root 4208336 2012-05-04 16:45 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 16:45 ./usr/share/man/man1/Atropos.1.gz
ants_1.9.2+svn680.dfsg-4~nd+1_i386.deb
-rwxr-xr-x root/root 4033752 2012-05-04 16:11 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 16:11 ./usr/share/man/man1/Atropos.1.gz
ants_1.9.2+svn680.dfsg-4~nd60+1_amd64.deb
ants_1.9.2+svn680.dfsg-4~nd60+1_i386.deb
ants_1.9.2+svn680.dfsg-4~nd70+1_amd64.deb
-rwxr-xr-x root/root 4208336 2012-05-04 13:17 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 13:17 ./usr/share/man/man1/Atropos.1.gz
ants_1.9.2+svn680.dfsg-4~nd70+1_i386.deb
-rwxr-xr-x root/root 4033752 2012-05-04 12:43 ./usr/lib/ants/Atropos
-rw-r--r-- root/root 3183 2012-05-04 12:43 ./usr/share/man/man1/Atropos.1.gz
As a resolution to this -- upgrade to wheezy would be the "simplest"
resolution. I will try to finally expedite preparation of wheezy NeuroDebian
VM so you could take advantage of recent versions of core libraries etc
2. antsRegistration
this one was added in
commit c53e44c093f7c96d18d0dd5f53e572b4341c3db5
Author: ntustison <ntustison at fd2da0a4-d968-48df-9cb5-d8c496287cbf>
Date: Fri Dec 30 00:44:51 2011 +0000
ENH: Adding new registration stuff.
git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1060 fd2da0a4-d968-48df-9cb5-d8c496287cbf
so -- quite later (revision 1060) than what we provide in NeuroDebian ATM.
Time permitting, I will start working on preparing freshier version of ANTs
(per Brian's blessing most probably rev 1408. but that would require recent ITK
(4.2)
> Is this due to an incompatibility between current neurodebian/ANTs
> versions?
> I have successfully used template creation as well as various
> normalization scripts within ANTs.
> Thank you for any comments! (for more details, please see below)
> Christian
> *********
> Current setup:
> VirtualBox 4.1.22 on�Windows 7
> NeuroDebian VM version: 6.0.5 amd64 (updated)
> ANTs version: 1.9.2+svn680.dfsg-3~nd60+1
> Synaptic indicates the following files are installed:
> /.
> /usr
> /usr/bin
> /usr/bin/ANTS
> /usr/bin/WarpImageMultiTransform
> /usr/lib
> /usr/lib/ants
> /usr/lib/ants/ANTS
> /usr/lib/ants/ANTSAverage2DAffine.sh
> /usr/lib/ants/ANTSAverage3DAffine.sh
> /usr/lib/ants/ANTSIntegrateVectorField
> /usr/lib/ants/ANTSJacobian
> /usr/lib/ants/ANTSUseDeformationFieldToGetAffineTransform
> /usr/lib/ants/ANTSUseLandmarkImagesToGetAffineTransform
> /usr/lib/ants/ANTSpexec.sh
> /usr/lib/ants/AverageImages
> /usr/lib/ants/AverageTensorImages
> /usr/lib/ants/ClusterImageStatistics
> /usr/lib/ants/ComposeMultiTransform
> /usr/lib/ants/ConvertImagePixelType
> /usr/lib/ants/ConvertScalarImageToRGB
> /usr/lib/ants/ConvertToJpg
> /usr/lib/ants/CopyImageHeaderInformation
> /usr/lib/ants/CreateWarpedGridImage
> /usr/lib/ants/ExtractSliceFromImage
> /usr/lib/ants/ImageCompare
> /usr/lib/ants/ImageMath
> /usr/lib/ants/ImageSetStatistics
> /usr/lib/ants/KellySlater
> /usr/lib/ants/LabelClustersUniquely
> /usr/lib/ants/LabelOverlapMeasures
> /usr/lib/ants/LaplacianThickness
> /usr/lib/ants/MeasureImageSimilarity
> /usr/lib/ants/MeasureMinMaxMean
> /usr/lib/ants/MemoryTest
> /usr/lib/ants/MultiplyImages
> /usr/lib/ants/N3BiasFieldCorrection
> /usr/lib/ants/N4BiasFieldCorrection
> /usr/lib/ants/PermuteFlipImageOrientationAxes
> /usr/lib/ants/PrintHeader
> /usr/lib/ants/ReorientTensorImage
> /usr/lib/ants/ResampleImage
> /usr/lib/ants/ResampleImageBySpacing
> /usr/lib/ants/ResetDirection
> /usr/lib/ants/SetDirectionByMatrix
> /usr/lib/ants/SetOrigin
> /usr/lib/ants/SetSpacing
> /usr/lib/ants/SmoothImage
> /usr/lib/ants/StackSlices
> /usr/lib/ants/SurfaceBasedSmoothing
> /usr/lib/ants/SurfaceCurvature
> /usr/lib/ants/ThresholdImage
> /usr/lib/ants/TileImages
> /usr/lib/ants/WarpImageMultiTransform
> /usr/lib/ants/WarpTensorImageMultiTransform
> /usr/lib/ants/WarpTimeSeriesImageMultiTransform
> /usr/lib/ants/ants.sh
> /usr/lib/ants/antsIntroduction.sh
> /usr/lib/ants/antsaffine.sh
> /usr/lib/ants/antsbashstats.sh
> /usr/lib/ants/antsdeformationmag.sh
> /usr/lib/ants/antsqsub.sh
> /usr/lib/ants/antswithdt.sh
> /usr/lib/ants/buildtemplateparallel.sh
> /usr/lib/ants/geodesicinterpolation.sh
> /usr/lib/ants/guidedregistration.sh
> /usr/lib/ants/landmarkmatch.sh
> /usr/lib/ants/lohmann.sh
> /usr/lib/ants/optimalsmooth.sh
> /usr/lib/ants/phantomstudy.sh
> /usr/lib/ants/[1]registerimages.pl
> /usr/lib/ants/[2]runprogramonimageset.pl
> /usr/lib/ants/shapeupdatetotemplate.sh
> /usr/lib/ants/submitexperimentalbuild.sh
> /usr/lib/ants/sygnccavg.sh
> /usr/lib/ants/thickstudy.sh
> /usr/lib/ants/waitForSGEQJobs.pl
> /usr/lib/ants/[3]warpimages.pl
> /usr/lib/ants/[4]weightedaverage.pl
> /usr/lib/ants/weightedaverage.sh
> /usr/share
> /usr/share/doc
> /usr/share/doc/ants
> /usr/share/doc/ants/README.Debian
> /usr/share/doc/ants/README.txt.gz
> /usr/share/doc/ants/changelog.Debian.gz
> /usr/share/doc/ants/copyright
> /usr/share/lintian
> /usr/share/lintian/overrides
> /usr/share/lintian/overrides/ants
> /usr/share/man
> /usr/share/man/man1
> /usr/share/man/man1/ANTS.1.gz
> /usr/share/man/man1/ANTSIntegrateVectorField.1.gz
> /usr/share/man/man1/ANTSJacobian.1.gz
> /usr/share/man/man1/ANTSUseDeformationFieldToGetAffineTransform.1.gz
> /usr/share/man/man1/ANTSUseLandmarkImagesToGetAffineTransform.1.gz
> /usr/share/man/man1/AverageImages.1.gz
> /usr/share/man/man1/AverageTensorImages.1.gz
> /usr/share/man/man1/ClusterImageStatistics.1.gz
> /usr/share/man/man1/ComposeMultiTransform.1.gz
> /usr/share/man/man1/ConvertImagePixelType.1.gz
> /usr/share/man/man1/ConvertScalarImageToRGB.1.gz
> /usr/share/man/man1/ConvertToJpg.1.gz
> /usr/share/man/man1/CopyImageHeaderInformation.1.gz
> /usr/share/man/man1/CreateWarpedGridImage.1.gz
> /usr/share/man/man1/ExtractSliceFromImage.1.gz
> /usr/share/man/man1/ImageCompare.1.gz
> /usr/share/man/man1/ImageMath.1.gz
> /usr/share/man/man1/ImageSetStatistics.1.gz
> /usr/share/man/man1/KellySlater.1.gz
> /usr/share/man/man1/LabelClustersUniquely.1.gz
> /usr/share/man/man1/LabelOverlapMeasures.1.gz
> /usr/share/man/man1/LaplacianThickness.1.gz
> /usr/share/man/man1/MeasureImageSimilarity.1.gz
> /usr/share/man/man1/MeasureMinMaxMean.1.gz
> /usr/share/man/man1/MemoryTest.1.gz
> /usr/share/man/man1/MultiplyImages.1.gz
> /usr/share/man/man1/N3BiasFieldCorrection.1.gz
> /usr/share/man/man1/N4BiasFieldCorrection.1.gz
> /usr/share/man/man1/PermuteFlipImageOrientationAxes.1.gz
> /usr/share/man/man1/PrintHeader.1.gz
> /usr/share/man/man1/ReorientTensorImage.1.gz
> /usr/share/man/man1/ResampleImage.1.gz
> /usr/share/man/man1/ResampleImageBySpacing.1.gz
> /usr/share/man/man1/ResetDirection.1.gz
> /usr/share/man/man1/SetDirectionByMatrix.1.gz
> /usr/share/man/man1/SetOrigin.1.gz
> /usr/share/man/man1/SetSpacing.1.gz
> /usr/share/man/man1/SmoothImage.1.gz
> /usr/share/man/man1/StackSlices.1.gz
> /usr/share/man/man1/SurfaceBasedSmoothing.1.gz
> /usr/share/man/man1/SurfaceCurvature.1.gz
> /usr/share/man/man1/ThresholdImage.1.gz
> /usr/share/man/man1/TileImages.1.gz
> /usr/share/man/man1/WarpImageMultiTransform.1.gz
> /usr/share/man/man1/WarpTensorImageMultiTransform.1.gz
> /usr/share/man/man1/WarpTimeSeriesImageMultiTransform.1.gz
> References
> Visible links
> 1. http://registerimages.pl/
> 2. http://runprogramonimageset.pl/
> 3. http://warpimages.pl/
> 4. http://weightedaverage.pl/
> _______________________________________________
> Neurodebian-users mailing list
> Neurodebian-users at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
--
Yaroslav O. Halchenko
Postdoctoral Fellow, Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
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