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20120131 - ANTS: Advanced Normalization ToolS

Try out ANTS Tool

 

A. Build

A.1. Error

Following instructions from http://picsl.upenn.edu/ANTS/download.php

2012 02 02: svn update -r r1106 ( Revision 1107 is broken. )

CMake magic does not work for now.  

CMake Magic

Hi Regina,

You need to update as I'm currently testing on a 5-modality
3-D data set and I discovered that the rigid initialization
wasn't being performed properly in the ants multivariate
template building script.

Regarding $ANTSPATH---it should point to your build directory.
The cmake magic should copy all your scripts to the build
directory and that's where all your executables should
reside (at least that is the intent). If not, then something
unexpected happened.

Nick

A.2. Temporary solution

CMAKE Magic?

Don't we need to set CMAKE_INSTALL_PREFIX properly?

ANTS/Examples/CMakeLists.txt
MESSAGE("CMAKE_INSTALL_PREFIX::: ${CMAKE_INSTALL_PREFIX}")
install(PROGRAMS ../Scripts/ants.sh  ../Scripts/basic_ants_example.sh
                ../Scripts/antsIntroduction.sh
                ../Scripts/antsaffine.sh
        ../Scripts/waitForXGridJobs.pl
                ../Scripts/ANTSAverage2DAffine.sh ../Scripts/ANTSAverage3DAffine.sh
                ../Scripts/buildtemplateparallel.sh ../Scripts/ANTSpexec.sh
                ../Scripts/waitForSGEQJobs.pl DESTINATION bin
                PERMISSIONS  OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
                CONFIGURATIONS  Release )

[eunyokim@wundt build]$ make
[ 47%] Built target ITKv4
[ 47%] Performing forcebuild step for 'ANTS'
[ 47%] Performing build step for 'ANTS'
CMAKE_INSTALL_PREFIX::: /usr/local
-- Configuring done
-- Generating done

 

[eunyokim@wundt build]$ find ../ANTS/ -type f -print |xargs grep -n "CMAKE_INSTALL_PREFIX"
../ANTS//CMake/PreventInBuildInstalls.cmake:2:string(TOLOWER "${CMAKE_INSTALL_PREFIX}" _PREFIX)
../ANTS//CMake/PreventInBuildInstalls.cmake:6: "The current CMAKE_INSTALL_PREFIX points at the build tree:\n"
../ANTS//CMake/PreventInBuildInstalls.cmake:7: " ${CMAKE_INSTALL_PREFIX}\n"
../ANTS//Examples/CMakeLists.txt:320:MESSAGE("CMAKE_INSTALL_PREFIX::: ${CMAKE_INSTALL_PREFIX}")
../ANTS//SuperBuild.cmake:154: CMAKE_INSTALL_PREFIX:PATH
../ANTS//SuperBuild/External_KWStyle.cmake:39: -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_BINARY_DIR}/Utils

 

Even specifying the CMAKE_INSTALL_PREFIX did not work..
/opt/cmake-2.8.6-Darwin64-universal/bin/cmake ../ANTS/ -DCMAKE_INSTALL_PREFIX:PATH=/ipldev/scratch/eunyokim/src/ANTSFromGitHub/build/bin
 
[eunyokim@wundt build]$ make 
[ 47%] Built target ITKv4
[ 47%] Performing forcebuild step for 'ANTS'
[ 47%] Performing build step for 'ANTS'
CMAKE_INSTALL_PREFIX::: /ipldev/scratch/eunyokim/src/ANTSFromGitHub/build/bin
-- Configuring done
-- Generating done


[eunyokim@wundt build]$ ls bin/
ANTS*                                        LabelOverlapMeasures*
ANTSIntegrateVectorField*                    LaplacianThickness*
ANTSIntegrateVelocityField*                  MeasureImageSimilarity*
ANTSJacobian*                                MeasureMinMaxMean*
ANTSUseDeformationFieldToGetAffineTransform* MemoryTest*
ANTSUseLandmarkImagesToGetAffineTransform*   MultiplyImages*
Atropos*                                     N3BiasFieldCorrection*
AtroposMin*                                  N4BiasFieldCorrection*
AverageAffineTransform*                      PasteImageIntoImage*
AverageImages*                               PermuteFlipImageOrientationAxes*
AverageTensorImages*                         PrintHeader*
ClusterImageStatistics*                      ReorientTensorImage*
ComposeMultiTransform*                       ResampleImage*
ConvertImagePixelType*                       ResampleImageBySpacing*
ConvertScalarImageToRGB*                     ResetDirection*
ConvertToJpg*                                SetDirectionByMatrix*
CopyImageHeaderInformation*                  SetOrigin*
CreateDTICohort*                             SetSpacing*
CreateImage*                                 SmoothImage*
CreateWarpedGridImage*                       StackSlices*
ExtractRegionFromImage*                      SurfaceBasedSmoothing*
ExtractRegionFromImageByMask*                SurfaceCurvature*
ExtractSliceFromImage*                       ThresholdImage*
H5detect*                                    TileImages*
H5make_libsettings*                          WarpImageMultiTransform*
ImageCompare*                                WarpTensorImageMultiTransform*
ImageMath*                                   WarpTimeSeriesImageMultiTransform*
ImageSetStatistics*                          antsApplyTransforms*
KellyKapowski*                               antsMotionCorr*
KellySlater*                                 antsRegistration*
LabelClustersUniquely*                       itkTestDriver*
LabelGeometryMeasures*                       sccan*

Ugly solution for now

export ANTSScriptPATH=/ipldev/scratch/eunyokim/src/ANTSFromGitHub/ANTS/Scripts/

ANTS/Scripts/antsMultivariateTemplateConstruction.sh
PEXEC=${ANTSScriptPATH}ANTSpexec.sh
SGE=${ANTSScriptPATH}waitForSGEQJobs.pl
PBS=${ANTSScriptPATH}waitForPBSQJobs.pl
XGRID=${ANTSScriptPATH}waitForXGridJobs.pl

B. Testing with five subjects

First Trial

bash -x /ipldev/scratch/eunyokim/src/ANTSFromGitHub/ANTS/Scripts/antsMultivariateTemplateConstruction.sh -d 3 -c 0 -k 2 -o ./ANTSOut -z /ipldev/scratch/eunyokim/src/BRAINS20111028/build-Darwin/ReferenceAtlas-build/Atlas/Atlas_20120104/template_t1.nii.gz  /ipldev/scratch/eunyokim/src/ANTS/trial/fiveSubjectOnly.csv  2>&1|tee result.log 

The above script is running (Started on Friday 10th Feb)

Wierd 1. The script is deleting the csv file I provided. ( rm -f ${IMAGESETVARIABLE} ). The script delete only when the script failed. yeat, that's weird too.

Wierd 2. The same script in different location DOES NOT WORK.

It looks like -d, -c, -z options are mendatory not optional

fiveSubjectsTest.csv:::

/paulsen/IPIG/predict_3T_MR/site-054/0284/20715/10_AUTO.NN3Tv20110418/20715_AVG_T1.nii.gz,/paulsen/IPIG/predict_3T_MR/site-054/0284/20715/10_AUTO.NN3Tv20110418/20715_AVG_T2.nii.gz
/paulsen/IPIG/predict_3T_MR/site-024/0644/84123/10_AUTO.NN3Tv20110418/84123_AVG_T1.nii.gz,/paulsen/IPIG/predict_3T_MR/site-024/0644/84123/10_AUTO.NN3Tv20110418/84123_AVG_T2.nii.gz
/paulsen/IPIG/predict_3T_MR/site-024/0326/10335/10_AUTO.NN3Tv20110418/10335_AVG_T1.nii.gz,/paulsen/IPIG/predict_3T_MR/site-024/0326/10335/10_AUTO.NN3Tv20110418/10335_AVG_T2.nii.gz
/paulsen/IPIG/predict_3T_MR/site-024/0241/37022/10_AUTO.NN3Tv20110418/37022_AVG_T1.nii.gz,/paulsen/IPIG/predict_3T_MR/site-024/0241/37022/10_AUTO.NN3Tv20110418/37022_AVG_T2.nii.gz
/paulsen/IPIG/predict_3T_MR/site-024/0652/23958/10_AUTO.NN3Tv20110418/23958_AVG_T1.nii.gz,/paulsen/IPIG/predict_3T_MR/site-024/0652/23958/10_AUTO.NN3Tv20110418/23958_AVG_T2.nii.gz

Results: Four Iterations pdf

C. Testing with 30 subjects

The relative path would NOT work: Giving un-related error.

Specifying 12 core to use will KILL your machine. Don't do it.

Running script

 bash -x /ipldev/scratch/eunyokim/src/ANTSFromGitHub/ANTS/Scripts/antsMultivariateTemplateConstruction.sh -d 3 -c 2 -j 4  -k 2 -o ./ANTS -z /ipldev/scratch/eunyokim/src/BRAINS20111028/build-Darwin/ReferenceAtlas-build/Atlas/Atlas_20120104/templa_t1.nii.gz  /hjohnson/HDNI/PREDICT_TRAINING/regina_ann/TrainingModels/ANTSTrails/30Subjects/30Subjects.csv 2>&1|tee logInTheBuild.txt

ANTS trial result with 30 subjects:

What do you think?!

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