WORKDIR=/workarea/igilab/data/qayyum/hccminv_jeet/workdir

job881893_Reg-RF:
	cd $(WORKDIR)/881893;c3d 881893.Art.gray.nii.gz 881893.Art.labels.nii.gz -copy-transform -o 881893.Art.labels_hdr.nii.gz
	cd $(WORKDIR)/881893;c3d 881893.Del.gray.nii.gz 881893.Del.labels.nii.gz -copy-transform -o 881893.Del.labels_hdr.nii.gz
	cd $(WORKDIR)/881893;c3d 881893.Art.gray.nii.gz -orient RAI -o 881893.Art.gray.nii.gz            
	cd $(WORKDIR)/881893;c3d 881893.Art.labels_hdr.nii.gz -orient RAI -o 881893.Art.labels_hdr.nii.gz  
	cd $(WORKDIR)/881893;c3d 881893.Del.gray.nii.gz -orient RAI -o 881893.Del.gray.nii.gz          
	cd $(WORKDIR)/881893;c3d 881893.Del.labels_hdr.nii.gz -orient RAI -o 881893.Del.labels_hdr.nii.gz
	cd $(WORKDIR)/881893;c3d -verbose 881893.Art.gray.nii.gz 881893.Art.labels_hdr.nii.gz -binarize -multiply -o 881893.Art.strip.nii.gz            
	cd $(WORKDIR)/881893;c3d -verbose 881893.Del.gray.nii.gz 881893.Del.labels_hdr.nii.gz -binarize -multiply -o 881893.Del.strip.nii.gz           
	cd $(WORKDIR)/881893;/opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ANTS 3 -m CC[881893.Art.strip.nii.gz,881893.Del.strip.nii.gz,1,5] -o hellotarget -i 0 --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000  
	cd $(WORKDIR)/881893;/opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/WarpImageMultiTransform 3 881893.Del.gray.nii.gz 881893.Del.graydeformed.nii.gz hellotargetAffine.txt -R 881893.Art.gray.nii.gz 
	cd $(WORKDIR)/881893;/opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/WarpImageMultiTransform 3 881893.Del.labels_hdr.nii.gz 881893.Del.labelsdeformed.nii.gz hellotargetAffine.txt -R 881893.Art.gray.nii.gz 
	cd $(WORKDIR)/881893;c3d -verbose 881893.Art.labels_hdr.nii.gz  -binarize 881893.Del.labelsdeformed.nii.gz -binarize -overlap 1 
	cd $(WORKDIR)/881893;c3d 881893.Art.labels_hdr.nii.gz -binarize -o 881893.Art.labels_hdr_mask.nii.gz
	cd $(WORKDIR)/881893;../../createFeatureImages.sh -d 3 -x 881893.Art.labels_hdr_mask.nii.gz -l 1 -n Del -a 881893.Del.graydeformed.nii.gz -t ../../Del.histogramtemplate_NORMALIZED.nii.gz -n Art -a 881893.Art.gray.nii.gz -t ../../Art.histogramtemplate_NORMALIZED.nii.gz -o ./texture -r 1 -r 3 -r 5 -s 2 -b 3
	cd $(WORKDIR)/881893;../../applyTumorSegmentationModel.sh -d 3 -x 881893.Art.labels_hdr_mask.nii.gz -l 1 -n Del -a 881893.Del.graydeformed.nii.gz -t ../../Del.histogramtemplate_NORMALIZED.nii.gz -n Art -a 881893.Art.gray.nii.gz  -t ../../Art.histogramtemplate_NORMALIZED.nii.gz -o ./texture -r 1 -r 3 -r 5 -s 2 -b 3 -m ../../GMM_FeatureModel.RData
	cd $(WORKDIR)/881893;/opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 LABELS.GMM.reg.nii.gz MostLikely 0 textureRF_POSTERIORS*.nii.gz
	cd $(WORKDIR)/881893;c3d LABELS.GMM.reg.nii.gz LABELS.GMM.reg.nii.gz -lstat > VolStat.lstat.txt; sed "s/\s\+/,/g" VolStat.lstat.txt > VolStat.lstat.csv


job786189_Reg-RF:
	cd $(WORKDIR)/786189;c3d 786189.Art.gray.nii.gz 786189.Art.labels.nii.gz -copy-transform -o 786189.Art.labels_hdr.nii.gz
	cd $(WORKDIR)/786189;c3d 786189.Del.gray.nii.gz 786189.Del.labels.nii.gz -copy-transform -o 786189.Del.labels_hdr.nii.gz
	cd $(WORKDIR)/786189;c3d 786189.Art.gray.nii.gz -orient RAI -o 786189.Art.gray.nii.gz            
	cd $(WORKDIR)/786189;c3d 786189.Art.labels_hdr.nii.gz -orient RAI -o 786189.Art.labels_hdr.nii.gz  
	cd $(WORKDIR)/786189;c3d 786189.Del.gray.nii.gz -orient RAI -o 786189.Del.gray.nii.gz          
	cd $(WORKDIR)/786189;c3d 786189.Del.labels_hdr.nii.gz -orient RAI -o 786189.Del.labels_hdr.nii.gz
	cd $(WORKDIR)/786189;c3d -verbose 786189.Art.gray.nii.gz 786189.Art.labels_hdr.nii.gz -binarize -multiply -o 786189.Art.strip.nii.gz            
	cd $(WORKDIR)/786189;c3d -verbose 786189.Del.gray.nii.gz 786189.Del.labels_hdr.nii.gz -binarize -multiply -o 786189.Del.strip.nii.gz           
	cd $(WORKDIR)/786189;/opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ANTS 3 -m CC[786189.Art.strip.nii.gz,786189.Del.strip.nii.gz,1,5] -o hellotarget -i 0 --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000  
	cd $(WORKDIR)/786189;/opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/WarpImageMultiTransform 3 786189.Del.gray.nii.gz 786189.Del.graydeformed.nii.gz hellotargetAffine.txt -R 786189.Art.gray.nii.gz 
	cd $(WORKDIR)/786189;/opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/WarpImageMultiTransform 3 786189.Del.labels_hdr.nii.gz 786189.Del.labelsdeformed.nii.gz hellotargetAffine.txt -R 786189.Art.gray.nii.gz 
	cd $(WORKDIR)/786189;c3d -verbose 786189.Art.labels_hdr.nii.gz  -binarize 786189.Del.labelsdeformed.nii.gz -binarize -overlap 1 
	cd $(WORKDIR)/786189;c3d 786189.Art.labels_hdr.nii.gz -binarize -o 786189.Art.labels_hdr_mask.nii.gz
	cd $(WORKDIR)/786189;../../createFeatureImages.sh -d 3 -x 786189.Art.labels_hdr_mask.nii.gz -l 1 -n Del -a 786189.Del.graydeformed.nii.gz -t ../../Del.histogramtemplate_NORMALIZED.nii.gz -n Art -a 786189.Art.gray.nii.gz -t ../../Art.histogramtemplate_NORMALIZED.nii.gz -o ./texture -r 1 -r 3 -r 5 -s 2 -b 3
	cd $(WORKDIR)/786189;../../applyTumorSegmentationModel.sh -d 3 -x 786189.Art.labels_hdr_mask.nii.gz -l 1 -n Del -a 786189.Del.graydeformed.nii.gz -t ../../Del.histogramtemplate_NORMALIZED.nii.gz -n Art -a 786189.Art.gray.nii.gz  -t ../../Art.histogramtemplate_NORMALIZED.nii.gz -o ./texture -r 1 -r 3 -r 5 -s 2 -b 3 -m ../../GMM_FeatureModel.RData
	cd $(WORKDIR)/786189;/opt/apps/ANTsR/dev//ANTsR_src/ANTsR/src/ANTS/ANTS-build//bin/ImageMath 3 LABELS.GMM.reg.nii.gz MostLikely 0 textureRF_POSTERIORS*.nii.gz
	cd $(WORKDIR)/786189;c3d LABELS.GMM.reg.nii.gz LABELS.GMM.reg.nii.gz -lstat > VolStat.lstat.txt; sed "s/\s\+/,/g" VolStat.lstat.txt > VolStat.lstat.csv