### LiverSegmentationExample :grimacing: ### Usage * while [ 1 ] ; do make -f prediction.makefile -i -k -j 4 gmmfeature stats png predictors ; make -f prediction.makefile -i -k summary.pdf ;sleep 5 ; done An example image set from a single study needed as input to the random forest models is shown below. Mask.nii.gz | Pre.nii.gz | Art.nii.gz | Ven.nii.gz | Del.nii.gz ----------- | ----------- | ---------- | ---------- | ---------- ![mask](/DataSetupREADME/pdffig/mask.png) | ![pre](/DataSetupREADME/pdffig/precontrast.png) | ![art](/DataSetupREADME/pdffig/arterial.png) | ![ven](/DataSetupREADME/pdffig/venous.png) | ![del](/DataSetupREADME/pdffig/delay.png) Each image set should be in a separate directory and should follow the below naming convention *exactly*: ``` $ ls ImageDatabase/Predict0001/before/ Art.nii.gz Del.nii.gz Mask.nii.gz Pre.nii.gz Ven.nii.gz ``` ### Example Segmentation Output images are organized with respect to the model used for the segmentation $(WORKDIR)/%/$(RFMODEL)/LABELS.GMM.nii.gz RF Output | Mask.nii.gz | Pre.nii.gz | Art.nii.gz | Ven.nii.gz | Del.nii.gz ----------- | ----------- | ----------- | ---------- | ---------- | ---------- ![rf](/DataSetupREADME/pdffig/LABELS.GMM.png) | ![mask](/DataSetupREADME/pdffig/Mask.png) | ![pre](/DataSetupREADME/pdffig/Pre.png) | ![art](/DataSetupREADME/pdffig/Art.png) | ![ven](/DataSetupREADME/pdffig/Ven.png) | ![del](/DataSetupREADME/pdffig/Del.png) ``` innovador$ make -f prediction.makefile segmentation export SCRIPTSPATH=/workarea/fuentes/github/LiverSegmentationExample/Code; mkdir -p /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel; cd /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before; /workarea/fuentes/github/LiverSegmentationExample/Code/applyTumorSegmentationModel.sh -d 3 -x /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Mask.nii.gz -l 1 -n Pre -a /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Pre.nii.gz -n Art -a /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Art.nii.gz -n Ven -a /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Ven.nii.gz -n Del -a /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Del.nii.gz -r 1 -r 3 -r 5 -s 2 -b 3 -o /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texture -k /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel/ -m /workarea/fuentes/github/LiverSegmentationExample/workdir/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel Using applyTumorSegmentationModel with the following arguments: image dimension = 3 anatomical image = /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Pre.nii.gz /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Art.nii.gz /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Ven.nii.gz /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Del.nii.gz symmetric templates = cluster centers = image names = Pre Art Ven Del radii = 1 3 5 smoothing sigma = 2 priors = difference pairs = output prefix = /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texture --------------------- Running applyTumorSegmentationModel.sh on innovador --------------------- ###################################################################################### Create feature images ###################################################################################### /bin/bash /workarea/fuentes/github/LiverSegmentationExample/Code/createFeatureImages.sh -d 3 -x /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Mask.nii.gz -o /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texture -a /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Pre.nii.gz -n Pre -a /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Art.nii.gz -n Art -a /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Ven.nii.gz -n Ven -a /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Del.nii.gz -n Del -b 3 -r 1 -r 3 -r 5 -s 2 -l 1 python /workarea/fuentes/github/RandomForestHCCResponse/Code/slicecentroid.py --imagefile=/workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Mask.nii.gz centroid 48 BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Mask.nii.gz -erode 1 3x3x0vox -o /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.png END <<<<<<<<<<<<<<<<<<<< Using createFeatureImages with the following arguments: image dimension = 3 anatomical image = /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Pre.nii.gz /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Art.nii.gz /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Ven.nii.gz /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Del.nii.gz symmetric templates = symmetric template mask = cluster centers = image names = Pre Art Ven Del radii = 1 3 5 smoothing sigma = 2 priors = difference pairs = output prefix = /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texture --------------------- Running createFeatureImages.sh on innovador --------------------- BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz TruncateImageIntensity /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Pre.nii.gz 0.01 0.99 200 Lower quantile: 4.92341 Upper quantile: 98.548 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_RAWIMAGE.nii.gz m /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz operation m END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/TotalVariationDenoisingImage /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_RAWIMAGE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz .1 10 4 Iteration 1/10 Iteration 2/10 Iteration 3/10 Iteration 4/10 Iteration 5/10 Iteration 6/10 Iteration 7/10 Iteration 8/10 Iteration 9/10 Iteration 10/10 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Pre.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/GradientMagnitudeImageFilter /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_GRADIENT.nii.gz END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_GRADIENT.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map jet -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_GRADIENT.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_RESCALE.nii.gz RescaleImage /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 0 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz TruncateImageIntensity /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Art.nii.gz 0.01 0.99 200 Lower quantile: 11.731 Upper quantile: 210.617 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_RAWIMAGE.nii.gz m /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz operation m END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/TotalVariationDenoisingImage /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_RAWIMAGE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz .1 10 4 Iteration 1/10 Iteration 2/10 Iteration 3/10 Iteration 4/10 Iteration 5/10 Iteration 6/10 Iteration 7/10 Iteration 8/10 Iteration 9/10 Iteration 10/10 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Art.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/GradientMagnitudeImageFilter /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_GRADIENT.nii.gz END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_GRADIENT.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map jet -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_GRADIENT.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_RESCALE.nii.gz RescaleImage /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 0 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz TruncateImageIntensity /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Ven.nii.gz 0.01 0.99 200 Lower quantile: 22.4022 Upper quantile: 291.805 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_RAWIMAGE.nii.gz m /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz operation m END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/TotalVariationDenoisingImage /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_RAWIMAGE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz .1 10 4 Iteration 1/10 Iteration 2/10 Iteration 3/10 Iteration 4/10 Iteration 5/10 Iteration 6/10 Iteration 7/10 Iteration 8/10 Iteration 9/10 Iteration 10/10 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Ven.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/GradientMagnitudeImageFilter /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_GRADIENT.nii.gz END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_GRADIENT.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map jet -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_GRADIENT.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_RESCALE.nii.gz RescaleImage /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 0 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz TruncateImageIntensity /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Del.nii.gz 0.01 0.99 200 Lower quantile: 28.6886 Upper quantile: 199.64 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_RAWIMAGE.nii.gz m /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz operation m END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/TotalVariationDenoisingImage /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_RAWIMAGE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz .1 10 4 Iteration 1/10 Iteration 2/10 Iteration 3/10 Iteration 4/10 Iteration 5/10 Iteration 6/10 Iteration 7/10 Iteration 8/10 Iteration 9/10 Iteration 10/10 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Del.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/GradientMagnitudeImageFilter /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_GRADIENT.nii.gz END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_GRADIENT.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map jet -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_GRADIENT.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_RESCALE.nii.gz RescaleImage /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 0 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//Atropos -d 3 -a /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz -a /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz -a /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz -a /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz -i KMeans[3] -p Socrates[1] -x /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz -c [3,0] -k Gaussian -m [0.1,1x1x1] -o [/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureALL_ATROPOS_GMM.nii.gz,/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureALL_ATROPOS_GMM_POSTERIORS%d.nii.gz] Running Atropos for 3-dimensional images. Progress: Iteration 0 (of 3): posterior probability = 0 (annealing temperature = 1) Iteration 1 (of 3): posterior probability = 0.927787 (annealing temperature = 1) Writing output: Writing posterior image (class 1) Writing posterior image (class 2) Writing posterior image (class 3) AtroposSegmentationImageFilter (0x35be6a0) RTTI typeinfo: itk::ants::AtroposSegmentationImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 24763652 Debug: Off Object Name: Observers: IterationEvent(Command) Inputs: Primary: (0x35cb720) * _1: (0x35c86d0) _2: (0) _3: (0x35cbc00) _4: (0x35d36b0) _5: (0x35d69b0) Indexed Inputs: 0: Primary (0x35cb720) 1: _1 (0x35c86d0) 2: _2 (0) 3: _3 (0x35cbc00) 4: _4 (0x35d36b0) 5: _5 (0x35d69b0) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0xcd03f70) Indexed Outputs: 0: Primary (0xcd03f70) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 0 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 201 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Maximum number of iterations: 3 Convergence threshold: 0 Mask label: 1 Number of tissue classes: 3 Number of partial volume classes: 0 Minimize memory usage: false Initialization strategy: K means clustering Posterior probability formulation: Socrates initial annealing temperature = 1 annealing rate = 1 minimum annealing temperature = 0.1 MRF parameters MRF smoothing factor = 0.1 MRF radius = [1, 1, 1] Use asynchronous updating of the labels. ICM parameters maximum ICM code = 13 maximum number of ICM iterations = 1 No outlier handling. Tissue class 1: proportion = 0.113572 GaussianListSampleFunction (0x35ce640) mean = [20.247511619853867, 62.830234531493744, 130.742753798021, 104.81860343827118], covariance = [170.423, 135.114, 42.4748, 41.2019; 135.114, 969.003, 857.969, 358.473; 42.4748, 857.969, 3197.68, 981.817; 41.2019, 358.473, 981.817, 958.299] Tissue class 2: proportion = 0.35158 GaussianListSampleFunction (0x35cbec0) mean = [38.719134389124264, 99.01839596080245, 154.70450786751667, 118.06995289856432], covariance = [39.8733, 67.3966, 48.271, 14.598; 67.3966, 1367.55, 942.452, 401.79; 48.271, 942.452, 2536.03, 933.964; 14.598, 401.79, 933.964, 739.593] Tissue class 3: proportion = 0.534351 GaussianListSampleFunction (0x35d7e60) mean = [50.08857647032519, 88.53461968640492, 192.98343826856376, 122.64284556259045], covariance = [42.4123, -1.80766, 18.7124, 5.10375; -1.80766, 260.679, -48.3559, 22.6462; 18.7124, -48.3559, 461.408, 126.509; 5.10375, 22.6462, 126.509, 166.268] Elapsed time: 167.05 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureALL_ATROPOS_GMM.nii.gz -slice z 48 -dup -oli /workarea/fuentes/github/RandomForestHCCResponse/Code/dfltlabels.txt 1.0 -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureALL_ATROPOS_GMM.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texture_DENOISE.nii.gz END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/FitCTContrastTransportModel /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texture_DENOISE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISE END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEPreArtDeriv.nii.gz -slice z 48 -clip -inf inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEPreArtDeriv.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEArtVenDeriv.nii.gz -slice z 48 -clip -inf inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEArtVenDeriv.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEVenDelDeriv.nii.gz -slice z 48 -clip -inf inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEVenDelDeriv.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEAreaUnderCurve.nii.gz -slice z 48 -clip -inf inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEAreaUnderCurve.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEArtDelDeriv.nii.gz -slice z 48 -clip -inf inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDENOISEArtDelDeriv.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 0 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_1.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 4 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_1.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 5 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 7 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 0 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_3.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 4 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_3.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 5 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 7 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 0 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_5.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_MEAN_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 4 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_5.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SIGMA_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 5 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_5.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_SKEWNESS_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz 7 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_5.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ENTROPY_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 0 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_1.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 4 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_1.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 5 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 7 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 0 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_3.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 4 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_3.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 5 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 7 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 0 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_5.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_MEAN_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 4 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_5.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SIGMA_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 5 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_5.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_SKEWNESS_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz 7 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_5.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ENTROPY_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 0 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_1.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 4 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_1.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 5 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 7 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 0 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_3.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 4 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_3.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 5 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 7 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 0 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_5.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_MEAN_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 4 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_5.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SIGMA_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 5 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_5.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_SKEWNESS_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz 7 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_5.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ENTROPY_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 0 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_1.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 4 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_1.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 5 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_1.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 7 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 0 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_3.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 4 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_3.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 5 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_3.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 7 3 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 0 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_5.nii.gz -slice z 48 -clip 0 200 -pad 1x0x0vox 0x0x0vox 200 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_MEAN_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 4 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_5.nii.gz -slice z 48 -clip 0 25 -pad 1x0x0vox 0x0x0vox 25 -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SIGMA_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 5 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_5.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_SKEWNESS_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_5.nii.gz NeighborhoodStats /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz 7 5 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_5.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ENTROPY_RADIUS_5.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz 0 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz m /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz operation m END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz Normalize /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> echo -c [0,0] impose no spatial regularization ?? -c [0,0] impose no spatial regularization ?? END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//Atropos -d 3 -a /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_DENOISE.nii.gz -i KMeans[3] -p Socrates[1] -x /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz -c [0,0] -k Gaussian -m [0.1,1x1x1] -o [/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM.nii.gz,/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_POSTERIORS%d.nii.gz] Running Atropos for 3-dimensional images. Progress: Writing output: Writing posterior image (class 1) Writing posterior image (class 2) Writing posterior image (class 3) AtroposSegmentationImageFilter (0x22ba630) RTTI typeinfo: itk::ants::AtroposSegmentationImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 678 Debug: Off Object Name: Observers: IterationEvent(Command) Inputs: Primary: (0x22c7690) * _1: (0x22c4660) Indexed Inputs: 0: Primary (0x22c7690) 1: _1 (0x22c4660) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x22beca0) Indexed Outputs: 0: Primary (0x22beca0) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 0 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 189 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Maximum number of iterations: 0 Convergence threshold: 0 Mask label: 1 Number of tissue classes: 3 Number of partial volume classes: 0 Minimize memory usage: false Initialization strategy: K means clustering Posterior probability formulation: Socrates initial annealing temperature = 1 annealing rate = 1 minimum annealing temperature = 0.1 MRF parameters MRF smoothing factor = 0.1 MRF radius = [1, 1, 1] Use asynchronous updating of the labels. ICM parameters maximum ICM code = 0 maximum number of ICM iterations = 1 No outlier handling. Tissue class 1: proportion = 0.0775653 GaussianListSampleFunction (0x22c7eb0) mean = [13.523450741698793], covariance = [62.8813] Tissue class 2: proportion = 0.406266 GaussianListSampleFunction (0x22c7950) mean = [37.344187684556864], covariance = [24.3912] Tissue class 3: proportion = 0.516169 GaussianListSampleFunction (0x22cddb0) mean = [51.26667187828106], covariance = [34.5574] Elapsed time: 11.2962 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/CannyEdgeDetectionImageFilter /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_CANNY.nii.gz Variance = 2 UpperThreshold = 0 LowerThreshold = 0 CannyEdgeDetectionImageFilter (0x36e01d0) RTTI typeinfo: itk::CannyEdgeDetectionImageFilter, itk::Image > Reference Count: 1 Modified Time: 701 Debug: Off Object Name: Observers: none Inputs: Primary: (0x36d6f60) * Indexed Inputs: 0: Primary (0x36d6f60) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x36e48a0) Indexed Outputs: 0: Primary (0x36e48a0) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 64 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Variance: [2, 2, 2] MaximumError: [0.01, 0.01, 0.01] UpperThreshold: 0 LowerThreshold: 0 Center: 13 Stride: 0x36e0510 GaussianFilter: DiscreteGaussianImageFilter (0x36e4c80) RTTI typeinfo: itk::DiscreteGaussianImageFilter, itk::Image > Reference Count: 1 Modified Time: 436 Debug: Off Object Name: Observers: none Inputs: Primary: (0x36d6f60) * Indexed Inputs: 0: Primary (0x36d6f60) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x36e9180) Indexed Outputs: 0: Primary (0x36e9180) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 75 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Variance: [2, 2, 2] MaximumError: [0.01, 0.01, 0.01] MaximumKernelWidth: 32 FilterDimensionality: 3 UseImageSpacing: 1 InternalNumberOfStreamDivisions: 9 MultiplyImageFilter: MultiplyImageFilter (0x36e9560) RTTI typeinfo: itk::MultiplyImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 693 Debug: Off Object Name: Observers: none Inputs: Primary: (0x36eddb0) * _1: (0x36ef160) Indexed Inputs: 0: Primary (0x36eddb0) 1: _1 (0x36ef160) Required Input Names: Primary NumberOfRequiredInputs: 2 Outputs: Primary: (0x36eda30) Indexed Outputs: 0: Primary (0x36eda30) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 86 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 InPlace: Off The input and output to this filter are the same type. The filter can be run in place. UpdateBuffer1: Image (0x36eddb0) RTTI typeinfo: itk::Image Reference Count: 2 Modified Time: 431 Debug: Off Object Name: Observers: none Source: (none) Source output name: (none) Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 0 UpdateMTime: 0 RealTimeStamp: 0 seconds LargestPossibleRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] BufferedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] RequestedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] Spacing: [0.664062, 0.664062, 2.5] Origin: [170, 170, -450] Direction: -1 0 0 0 -1 0 0 0 1 IndexToPointMatrix: -0.664062 0 0 0 -0.664062 0 0 0 2.5 PointToIndexMatrix: -1.50588 0 0 0 -1.50588 0 0 0 0.4 Inverse Direction: -1 0 0 0 -1 0 0 0 1 PixelContainer: ImportImageContainer (0x36ee070) RTTI typeinfo: itk::ImportImageContainer Reference Count: 1 Modified Time: 432 Debug: Off Object Name: Observers: none Pointer: 0x2aece563f010 Container manages memory: true Size: 24379392 Capacity: 24379392 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//GetConnectedComponentsFeatureImages 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_ END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> echo /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ThresholdImage 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 1 1 0 /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ThresholdImage 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 1 1 0 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM.nii.gz -thresh 1 1 1 0 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz -thresh .17 inf 1 0 -multiply -comp -thresh 1 1 1 0 -o /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz There are 312 connected components. Largest component has 4879 pixels. END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_CANNY.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_CANNY.nii.gz 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM.nii.gz -slice z 48 -dup -oli /workarea/fuentes/github/RandomForestHCCResponse/Code/dfltlabels.txt 1.0 -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_VOLUME_TO_SURFACE_AREA_RATIO.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_VOLUME_TO_SURFACE_AREA_RATIO.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_PHYSICAL_VOLUME.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_PHYSICAL_VOLUME.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_ECCENTRICITY.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_ECCENTRICITY.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_ELONGATION.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_ELONGATION.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_CANNY.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_CANNY.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_POSTERIORS1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_POSTERIORS1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_POSTERIORS2.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_POSTERIORS2.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_POSTERIORS3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texturePre_ATROPOS_GMM_POSTERIORS3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> echo -c [0,0] impose no spatial regularization ?? -c [0,0] impose no spatial regularization ?? END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//Atropos -d 3 -a /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_DENOISE.nii.gz -i KMeans[3] -p Socrates[1] -x /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz -c [0,0] -k Gaussian -m [0.1,1x1x1] -o [/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM.nii.gz,/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_POSTERIORS%d.nii.gz] Running Atropos for 3-dimensional images. Progress: Writing output: Writing posterior image (class 1) Writing posterior image (class 2) Writing posterior image (class 3) AtroposSegmentationImageFilter (0x2bf0630) RTTI typeinfo: itk::ants::AtroposSegmentationImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 678 Debug: Off Object Name: Observers: IterationEvent(Command) Inputs: Primary: (0x2bfd690) * _1: (0x2bfa660) Indexed Inputs: 0: Primary (0x2bfd690) 1: _1 (0x2bfa660) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x2bf4ca0) Indexed Outputs: 0: Primary (0x2bf4ca0) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 0 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 189 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Maximum number of iterations: 0 Convergence threshold: 0 Mask label: 1 Number of tissue classes: 3 Number of partial volume classes: 0 Minimize memory usage: false Initialization strategy: K means clustering Posterior probability formulation: Socrates initial annealing temperature = 1 annealing rate = 1 minimum annealing temperature = 0.1 MRF parameters MRF smoothing factor = 0.1 MRF radius = [1, 1, 1] Use asynchronous updating of the labels. ICM parameters maximum ICM code = 0 maximum number of ICM iterations = 1 No outlier handling. Tissue class 1: proportion = 0.202179 GaussianListSampleFunction (0x2bfdeb0) mean = [52.754389810451244], covariance = [226.96] Tissue class 2: proportion = 0.635699 GaussianListSampleFunction (0x2bfd950) mean = [88.52434997019799], covariance = [117.471] Tissue class 3: proportion = 0.162122 GaussianListSampleFunction (0x2c03db0) mean = [137.94951324607055], covariance = [433.537] Elapsed time: 11.0461 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/CannyEdgeDetectionImageFilter /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_CANNY.nii.gz Variance = 2 UpperThreshold = 0 LowerThreshold = 0 CannyEdgeDetectionImageFilter (0x2c991d0) RTTI typeinfo: itk::CannyEdgeDetectionImageFilter, itk::Image > Reference Count: 1 Modified Time: 701 Debug: Off Object Name: Observers: none Inputs: Primary: (0x2c8ff60) * Indexed Inputs: 0: Primary (0x2c8ff60) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x2c9d8a0) Indexed Outputs: 0: Primary (0x2c9d8a0) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 64 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Variance: [2, 2, 2] MaximumError: [0.01, 0.01, 0.01] UpperThreshold: 0 LowerThreshold: 0 Center: 13 Stride: 0x2c99510 GaussianFilter: DiscreteGaussianImageFilter (0x2c9dc80) RTTI typeinfo: itk::DiscreteGaussianImageFilter, itk::Image > Reference Count: 1 Modified Time: 436 Debug: Off Object Name: Observers: none Inputs: Primary: (0x2c8ff60) * Indexed Inputs: 0: Primary (0x2c8ff60) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x2ca2180) Indexed Outputs: 0: Primary (0x2ca2180) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 75 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Variance: [2, 2, 2] MaximumError: [0.01, 0.01, 0.01] MaximumKernelWidth: 32 FilterDimensionality: 3 UseImageSpacing: 1 InternalNumberOfStreamDivisions: 9 MultiplyImageFilter: MultiplyImageFilter (0x2ca2560) RTTI typeinfo: itk::MultiplyImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 693 Debug: Off Object Name: Observers: none Inputs: Primary: (0x2ca6db0) * _1: (0x2ca8160) Indexed Inputs: 0: Primary (0x2ca6db0) 1: _1 (0x2ca8160) Required Input Names: Primary NumberOfRequiredInputs: 2 Outputs: Primary: (0x2ca6a30) Indexed Outputs: 0: Primary (0x2ca6a30) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 86 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 InPlace: Off The input and output to this filter are the same type. The filter can be run in place. UpdateBuffer1: Image (0x2ca6db0) RTTI typeinfo: itk::Image Reference Count: 2 Modified Time: 431 Debug: Off Object Name: Observers: none Source: (none) Source output name: (none) Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 0 UpdateMTime: 0 RealTimeStamp: 0 seconds LargestPossibleRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] BufferedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] RequestedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] Spacing: [0.664062, 0.664062, 2.5] Origin: [170, 170, -450] Direction: -1 0 0 0 -1 0 0 0 1 IndexToPointMatrix: -0.664062 0 0 0 -0.664062 0 0 0 2.5 PointToIndexMatrix: -1.50588 0 0 0 -1.50588 0 0 0 0.4 Inverse Direction: -1 0 0 0 -1 0 0 0 1 PixelContainer: ImportImageContainer (0x2ca7070) RTTI typeinfo: itk::ImportImageContainer Reference Count: 1 Modified Time: 432 Debug: Off Object Name: Observers: none Pointer: 0x2b9e48c6d010 Container manages memory: true Size: 24379392 Capacity: 24379392 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//GetConnectedComponentsFeatureImages 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_ END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> echo /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ThresholdImage 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 1 1 0 /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ThresholdImage 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 1 1 0 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM.nii.gz -thresh 1 1 1 0 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz -thresh .17 inf 1 0 -multiply -comp -thresh 1 1 1 0 -o /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz There are 3281 connected components. Largest component has 98267 pixels. END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_CANNY.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_CANNY.nii.gz 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM.nii.gz -slice z 48 -dup -oli /workarea/fuentes/github/RandomForestHCCResponse/Code/dfltlabels.txt 1.0 -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_VOLUME_TO_SURFACE_AREA_RATIO.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_VOLUME_TO_SURFACE_AREA_RATIO.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_PHYSICAL_VOLUME.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_PHYSICAL_VOLUME.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_ECCENTRICITY.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_ECCENTRICITY.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_ELONGATION.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_ELONGATION.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_CANNY.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_CANNY.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_POSTERIORS1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_POSTERIORS1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_POSTERIORS2.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_POSTERIORS2.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_POSTERIORS3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureArt_ATROPOS_GMM_POSTERIORS3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> echo -c [0,0] impose no spatial regularization ?? -c [0,0] impose no spatial regularization ?? END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//Atropos -d 3 -a /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_DENOISE.nii.gz -i KMeans[3] -p Socrates[1] -x /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz -c [0,0] -k Gaussian -m [0.1,1x1x1] -o [/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM.nii.gz,/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_POSTERIORS%d.nii.gz] Running Atropos for 3-dimensional images. Progress: Writing output: Writing posterior image (class 1) Writing posterior image (class 2) Writing posterior image (class 3) AtroposSegmentationImageFilter (0x2dcd630) RTTI typeinfo: itk::ants::AtroposSegmentationImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 678 Debug: Off Object Name: Observers: IterationEvent(Command) Inputs: Primary: (0x2dda690) * _1: (0x2dd7660) Indexed Inputs: 0: Primary (0x2dda690) 1: _1 (0x2dd7660) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x2dd1ca0) Indexed Outputs: 0: Primary (0x2dd1ca0) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 0 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 189 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Maximum number of iterations: 0 Convergence threshold: 0 Mask label: 1 Number of tissue classes: 3 Number of partial volume classes: 0 Minimize memory usage: false Initialization strategy: K means clustering Posterior probability formulation: Socrates initial annealing temperature = 1 annealing rate = 1 minimum annealing temperature = 0.1 MRF parameters MRF smoothing factor = 0.1 MRF radius = [1, 1, 1] Use asynchronous updating of the labels. ICM parameters maximum ICM code = 0 maximum number of ICM iterations = 1 No outlier handling. Tissue class 1: proportion = 0.100097 GaussianListSampleFunction (0x2ddaeb0) mean = [69.33533750634548], covariance = [500.232] Tissue class 2: proportion = 0.234013 GaussianListSampleFunction (0x2dda950) mean = [143.46700108596409], covariance = [327.435] Tissue class 3: proportion = 0.66589 GaussianListSampleFunction (0x2de0db0) mean = [198.06256362572003], covariance = [321.39] Elapsed time: 11.1877 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/CannyEdgeDetectionImageFilter /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_CANNY.nii.gz Variance = 2 UpperThreshold = 0 LowerThreshold = 0 CannyEdgeDetectionImageFilter (0x28a81d0) RTTI typeinfo: itk::CannyEdgeDetectionImageFilter, itk::Image > Reference Count: 1 Modified Time: 701 Debug: Off Object Name: Observers: none Inputs: Primary: (0x289ef60) * Indexed Inputs: 0: Primary (0x289ef60) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x28ac8a0) Indexed Outputs: 0: Primary (0x28ac8a0) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 64 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Variance: [2, 2, 2] MaximumError: [0.01, 0.01, 0.01] UpperThreshold: 0 LowerThreshold: 0 Center: 13 Stride: 0x28a8510 GaussianFilter: DiscreteGaussianImageFilter (0x28acc80) RTTI typeinfo: itk::DiscreteGaussianImageFilter, itk::Image > Reference Count: 1 Modified Time: 436 Debug: Off Object Name: Observers: none Inputs: Primary: (0x289ef60) * Indexed Inputs: 0: Primary (0x289ef60) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x28b1180) Indexed Outputs: 0: Primary (0x28b1180) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 75 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Variance: [2, 2, 2] MaximumError: [0.01, 0.01, 0.01] MaximumKernelWidth: 32 FilterDimensionality: 3 UseImageSpacing: 1 InternalNumberOfStreamDivisions: 9 MultiplyImageFilter: MultiplyImageFilter (0x28b1560) RTTI typeinfo: itk::MultiplyImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 693 Debug: Off Object Name: Observers: none Inputs: Primary: (0x28b5db0) * _1: (0x28b7160) Indexed Inputs: 0: Primary (0x28b5db0) 1: _1 (0x28b7160) Required Input Names: Primary NumberOfRequiredInputs: 2 Outputs: Primary: (0x28b5a30) Indexed Outputs: 0: Primary (0x28b5a30) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 86 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 InPlace: Off The input and output to this filter are the same type. The filter can be run in place. UpdateBuffer1: Image (0x28b5db0) RTTI typeinfo: itk::Image Reference Count: 2 Modified Time: 431 Debug: Off Object Name: Observers: none Source: (none) Source output name: (none) Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 0 UpdateMTime: 0 RealTimeStamp: 0 seconds LargestPossibleRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] BufferedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] RequestedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] Spacing: [0.664062, 0.664062, 2.5] Origin: [170, 170, -450] Direction: -1 0 0 0 -1 0 0 0 1 IndexToPointMatrix: -0.664062 0 0 0 -0.664062 0 0 0 2.5 PointToIndexMatrix: -1.50588 0 0 0 -1.50588 0 0 0 0.4 Inverse Direction: -1 0 0 0 -1 0 0 0 1 PixelContainer: ImportImageContainer (0x28b6070) RTTI typeinfo: itk::ImportImageContainer Reference Count: 1 Modified Time: 432 Debug: Off Object Name: Observers: none Pointer: 0x2ad866ed4010 Container manages memory: true Size: 24379392 Capacity: 24379392 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//GetConnectedComponentsFeatureImages 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_ END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> echo /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ThresholdImage 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 1 1 0 /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ThresholdImage 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 1 1 0 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM.nii.gz -thresh 1 1 1 0 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz -thresh .17 inf 1 0 -multiply -comp -thresh 1 1 1 0 -o /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz There are 476 connected components. Largest component has 89342 pixels. END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_CANNY.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_CANNY.nii.gz 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM.nii.gz -slice z 48 -dup -oli /workarea/fuentes/github/RandomForestHCCResponse/Code/dfltlabels.txt 1.0 -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_VOLUME_TO_SURFACE_AREA_RATIO.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_VOLUME_TO_SURFACE_AREA_RATIO.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_PHYSICAL_VOLUME.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_PHYSICAL_VOLUME.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_ECCENTRICITY.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_ECCENTRICITY.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_ELONGATION.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_ELONGATION.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_CANNY.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_CANNY.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_POSTERIORS1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_POSTERIORS1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_POSTERIORS2.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_POSTERIORS2.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_POSTERIORS3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureVen_ATROPOS_GMM_POSTERIORS3.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> echo -c [0,0] impose no spatial regularization ?? -c [0,0] impose no spatial regularization ?? END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//Atropos -d 3 -a /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_DENOISE.nii.gz -i KMeans[3] -p Socrates[1] -x /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureMASKERODE.nii.gz -c [0,0] -k Gaussian -m [0.1,1x1x1] -o [/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM.nii.gz,/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_POSTERIORS%d.nii.gz] Running Atropos for 3-dimensional images. Progress: Writing output: Writing posterior image (class 1) Writing posterior image (class 2) Writing posterior image (class 3) AtroposSegmentationImageFilter (0x33a5630) RTTI typeinfo: itk::ants::AtroposSegmentationImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 678 Debug: Off Object Name: Observers: IterationEvent(Command) Inputs: Primary: (0x33b2690) * _1: (0x33af660) Indexed Inputs: 0: Primary (0x33b2690) 1: _1 (0x33af660) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x33a9ca0) Indexed Outputs: 0: Primary (0x33a9ca0) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 0 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 189 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Maximum number of iterations: 0 Convergence threshold: 0 Mask label: 1 Number of tissue classes: 3 Number of partial volume classes: 0 Minimize memory usage: false Initialization strategy: K means clustering Posterior probability formulation: Socrates initial annealing temperature = 1 annealing rate = 1 minimum annealing temperature = 0.1 MRF parameters MRF smoothing factor = 0.1 MRF radius = [1, 1, 1] Use asynchronous updating of the labels. ICM parameters maximum ICM code = 0 maximum number of ICM iterations = 1 No outlier handling. Tissue class 1: proportion = 0.0997714 GaussianListSampleFunction (0x33b2eb0) mean = [72.85082602325747], covariance = [281.166] Tissue class 2: proportion = 0.540581 GaussianListSampleFunction (0x33b2950) mean = [113.99142106413744], covariance = [75.0704] Tissue class 3: proportion = 0.359648 GaussianListSampleFunction (0x33b8db0) mean = [139.33493332351443], covariance = [126.395] Elapsed time: 11.3474 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/CannyEdgeDetectionImageFilter /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_CANNY.nii.gz Variance = 2 UpperThreshold = 0 LowerThreshold = 0 CannyEdgeDetectionImageFilter (0x28f31d0) RTTI typeinfo: itk::CannyEdgeDetectionImageFilter, itk::Image > Reference Count: 1 Modified Time: 701 Debug: Off Object Name: Observers: none Inputs: Primary: (0x28e9f60) * Indexed Inputs: 0: Primary (0x28e9f60) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x28f78a0) Indexed Outputs: 0: Primary (0x28f78a0) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 64 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Variance: [2, 2, 2] MaximumError: [0.01, 0.01, 0.01] UpperThreshold: 0 LowerThreshold: 0 Center: 13 Stride: 0x28f3510 GaussianFilter: DiscreteGaussianImageFilter (0x28f7c80) RTTI typeinfo: itk::DiscreteGaussianImageFilter, itk::Image > Reference Count: 1 Modified Time: 436 Debug: Off Object Name: Observers: none Inputs: Primary: (0x28e9f60) * Indexed Inputs: 0: Primary (0x28e9f60) Required Input Names: Primary NumberOfRequiredInputs: 1 Outputs: Primary: (0x28fc180) Indexed Outputs: 0: Primary (0x28fc180) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 75 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 Variance: [2, 2, 2] MaximumError: [0.01, 0.01, 0.01] MaximumKernelWidth: 32 FilterDimensionality: 3 UseImageSpacing: 1 InternalNumberOfStreamDivisions: 9 MultiplyImageFilter: MultiplyImageFilter (0x28fc560) RTTI typeinfo: itk::MultiplyImageFilter, itk::Image, itk::Image > Reference Count: 1 Modified Time: 693 Debug: Off Object Name: Observers: none Inputs: Primary: (0x2900db0) * _1: (0x2902160) Indexed Inputs: 0: Primary (0x2900db0) 1: _1 (0x2902160) Required Input Names: Primary NumberOfRequiredInputs: 2 Outputs: Primary: (0x2900a30) Indexed Outputs: 0: Primary (0x2900a30) NumberOfRequiredOutputs: 1 Number Of Threads: 24 ReleaseDataFlag: Off ReleaseDataBeforeUpdateFlag: Off AbortGenerateData: Off Progress: 1 Multithreader: RTTI typeinfo: itk::MultiThreader Reference Count: 1 Modified Time: 86 Debug: Off Object Name: Observers: none Thread Count: 24 Global Maximum Number Of Threads: 128 Global Default Number Of Threads: 24 CoordinateTolerance: 1e-06 DirectionTolerance: 1e-06 InPlace: Off The input and output to this filter are the same type. The filter can be run in place. UpdateBuffer1: Image (0x2900db0) RTTI typeinfo: itk::Image Reference Count: 2 Modified Time: 431 Debug: Off Object Name: Observers: none Source: (none) Source output name: (none) Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 0 UpdateMTime: 0 RealTimeStamp: 0 seconds LargestPossibleRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] BufferedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] RequestedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 93] Spacing: [0.664062, 0.664062, 2.5] Origin: [170, 170, -450] Direction: -1 0 0 0 -1 0 0 0 1 IndexToPointMatrix: -0.664062 0 0 0 -0.664062 0 0 0 2.5 PointToIndexMatrix: -1.50588 0 0 0 -1.50588 0 0 0 0.4 Inverse Direction: -1 0 0 0 -1 0 0 0 1 PixelContainer: ImportImageContainer (0x2901070) RTTI typeinfo: itk::ImportImageContainer Reference Count: 1 Modified Time: 432 Debug: Off Object Name: Observers: none Pointer: 0x2b4151f44010 Container manages memory: true Size: 24379392 Capacity: 24379392 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//GetConnectedComponentsFeatureImages 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_ END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> echo /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ThresholdImage 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 1 1 0 /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ThresholdImage 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 1 1 0 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM.nii.gz -thresh 1 1 1 0 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureNORMALIZED_DISTANCE.nii.gz -thresh .17 inf 1 0 -multiply -comp -thresh 1 1 1 0 -o /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz There are 2397 connected components. Largest component has 48487 pixels. END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_LABEL1_DISTANCE.nii.gz 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_CANNY.nii.gz MaurerDistance /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_CANNY.nii.gz 1 END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM.nii.gz -slice z 48 -dup -oli /workarea/fuentes/github/RandomForestHCCResponse/Code/dfltlabels.txt 1.0 -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_VOLUME_TO_SURFACE_AREA_RATIO.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_VOLUME_TO_SURFACE_AREA_RATIO.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_PHYSICAL_VOLUME.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_PHYSICAL_VOLUME.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_ECCENTRICITY.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_ECCENTRICITY.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_ELONGATION.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_ELONGATION.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_CANNY.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_CANNY.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_POSTERIORS1.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_POSTERIORS1.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_POSTERIORS2.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_POSTERIORS2.png END <<<<<<<<<<<<<<<<<<<< BEGIN >>>>>>>>>>>>>>>>>>>> c3d /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_POSTERIORS3.nii.gz -slice z 48 -clip 0 inf -color-map grey -type uchar -omc /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureDel_ATROPOS_GMM_POSTERIORS3.png END <<<<<<<<<<<<<<<<<<<< -------------------------------------------------------------------------------------- Done with creating feature images Script executed in 3051 seconds 0h 50m 51s -------------------------------------------------------------------------------------- ###################################################################################### Create csv file ###################################################################################### /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureFeatureImageList.csv Rscript /workarea/fuentes/github/LiverSegmentationExample/Code/createCSVFileFromModel.R /workarea/fuentes/github/LiverSegmentationExample/workdir/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Mask.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texture /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureFeatureImageList.csv BEGIN >>>>>>>>>>>>>>>>>>>> Rscript /workarea/fuentes/github/LiverSegmentationExample/Code/createCSVFileFromModel.R /workarea/fuentes/github/LiverSegmentationExample/workdir/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel /workarea/fuentes/github/LiverSegmentationExample/ImageDatabase/Predict0001/before/Mask.nii.gz /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/texture /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureFeatureImageList.csv randomForest 4.6-10 Type rfNews() to see new features/changes/bug fixes. END <<<<<<<<<<<<<<<<<<<< ###################################################################################### Apply the model ###################################################################################### Rscript /workarea/fuentes/github/LiverSegmentationExample/Code/applyModel.R 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureFeatureImageList.csv /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel/RF_POSTERIORS 1 BEGIN >>>>>>>>>>>>>>>>>>>> Rscript /workarea/fuentes/github/LiverSegmentationExample/Code/applyModel.R 3 /workarea/fuentes/github/LiverSegmentationExample/workdir/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/textureFeatureImageList.csv /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel/RF_POSTERIORS 1 Loading required package: Rcpp Loading required package: methods Loading required package: signal Loading required package: MASS Attaching package: ‘signal’ The following objects are masked from ‘package:stats’: filter, poly Loading required package: timeSeries Loading required package: timeDate Loading required package: mFilter Loading required package: robust Loading required package: fit.models Loading required package: lattice Loading required package: robustbase Loading required package: rrcov Loading required package: pcaPP Loading required package: mvtnorm Scalable Robust Estimators with High Breakdown Point (version 1.3-4) Loading required package: magic Loading required package: abind Loading required package: knitr Loading required package: pixmap Loading required package: misc3d Welcome to ANTsR randomForest 4.6-10 Type rfNews() to see new features/changes/bug fixes. Attaching package: ‘randomForest’ The following object is masked from ‘package:timeSeries’: outlier Loading required package: snow Reading feature image NORMALIZED_DISTANCE. Reading feature image Pre_DENOISE. Reading feature image Pre_GRADIENT. Reading feature image Art_DENOISE. Reading feature image Art_GRADIENT. Reading feature image Ven_DENOISE. Reading feature image Ven_GRADIENT. Reading feature image Del_DENOISE. Reading feature image Del_GRADIENT. Reading feature image DENOISEAreaUnderCurve. Reading feature image DENOISEPreArtDeriv. Reading feature image DENOISEArtVenDeriv. Reading feature image DENOISEVenDelDeriv. Reading feature image Pre_ATROPOS_GMM_POSTERIORS1. Reading feature image Pre_ATROPOS_GMM_POSTERIORS2. Reading feature image Pre_ATROPOS_GMM_POSTERIORS3. Reading feature image Pre_ATROPOS_GMM_LABEL1_DISTANCE. Reading feature image Pre_MEAN_RADIUS_1. Reading feature image Pre_MEAN_RADIUS_3. Reading feature image Pre_SIGMA_RADIUS_1. Reading feature image Pre_SIGMA_RADIUS_3. Reading feature image Pre_SKEWNESS_RADIUS_1. Reading feature image Pre_SKEWNESS_RADIUS_3. Reading feature image Art_ATROPOS_GMM_POSTERIORS1. Reading feature image Art_ATROPOS_GMM_POSTERIORS2. Reading feature image Art_ATROPOS_GMM_POSTERIORS3. Reading feature image Art_ATROPOS_GMM_LABEL1_DISTANCE. Reading feature image Art_MEAN_RADIUS_1. Reading feature image Art_MEAN_RADIUS_3. Reading feature image Art_SIGMA_RADIUS_1. Reading feature image Art_SIGMA_RADIUS_3. Reading feature image Art_SKEWNESS_RADIUS_1. Reading feature image Art_SKEWNESS_RADIUS_3. Reading feature image Ven_ATROPOS_GMM_POSTERIORS1. Reading feature image Ven_ATROPOS_GMM_POSTERIORS2. Reading feature image Ven_ATROPOS_GMM_POSTERIORS3. Reading feature image Ven_ATROPOS_GMM_LABEL1_DISTANCE. Reading feature image Ven_MEAN_RADIUS_1. Reading feature image Ven_MEAN_RADIUS_3. Reading feature image Ven_SIGMA_RADIUS_1. Reading feature image Ven_SIGMA_RADIUS_3. Reading feature image Ven_SKEWNESS_RADIUS_1. Reading feature image Ven_SKEWNESS_RADIUS_3. Reading feature image Del_ATROPOS_GMM_POSTERIORS1. Reading feature image Del_ATROPOS_GMM_POSTERIORS2. Reading feature image Del_ATROPOS_GMM_POSTERIORS3. Reading feature image Del_ATROPOS_GMM_LABEL1_DISTANCE. Reading feature image Del_MEAN_RADIUS_1. Reading feature image Del_MEAN_RADIUS_3. Reading feature image Del_SIGMA_RADIUS_1. Reading feature image Del_SIGMA_RADIUS_3. Reading feature image Del_SKEWNESS_RADIUS_1. Reading feature image Del_SKEWNESS_RADIUS_3. Prediction took 182.654 seconds. Writing /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel/RF_POSTERIORS1.nii.gz . Done writing image. PixelType: 'float' | Dimension: '3'. Writing /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel/RF_POSTERIORS2.nii.gz . Done writing image. PixelType: 'float' | Dimension: '3'. Writing /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel/RF_POSTERIORS3.nii.gz . Done writing image. PixelType: 'float' | Dimension: '3'. END <<<<<<<<<<<<<<<<<<<< -------------------------------------------------------------------------------------- Done with applying model Script executed in 3312 seconds 0h 55m 12s -------------------------------------------------------------------------------------- cd /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel; /opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin//ImageMath 3 LABELS.GMM.nii.gz MostLikely 0 RF_POSTERIORS*.nii.gz ``` ### Example Volume Calculation Given the segmented images, c3d is used to extract volume information. ``` innovador$ make -f prediction.makefile volume cd /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel; c3d LABELS.GMM.nii.gz LABELS.GMM.nii.gz -lstat > LABELS.GMM.VolStat.txt ; sed "s/\s\+/,/g" LABELS.GMM.VolStat.txt > LABELS.GMM.VolStat.csv innovador$ cat /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel/LABELS.GMM.VolStat.csv LabelID,Mean,StdD,Max,Min,Count,Vol(mm^3),Extent(Vox) ,0,0.00000,0.00000,0.00000,0.00000,22587824,24901854.558,512,512,93 ,1,1.00000,0.00000,1.00000,1.00000,1119734,1234446.187,270,299,71 ,2,2.00000,0.00000,2.00000,2.00000,609718,672181.125,243,280,69 ,3,3.00000,0.00000,3.00000,3.00000,62116,68479.531,144,176,40 ```