WORKDIR=/workarea/igilab/data/qayyum/tcga_ov/testarea


all: job20-13-0724 job22-13-0762 job25-13-0794 job27-13-0797 

job20-13-0724:
	cd $(WORKDIR)/20-13-0724;c3d 20-13-0724_grey.nii.gz 20-13-0724_labels.nii.gz -copy-transform -o 20-13-0724_labels.nii.gz
	cd $(WORKDIR)/20-13-0724;c3d 20-13-0724_grey.nii.gz -orient RAI -o 20-13-0724_grey.nii.gz
	cd $(WORKDIR)/20-13-0724;c3d 20-13-0724_labels.nii.gz -orient RAI -o 20-13-0724_labels.nii.gz
	cd $(WORKDIR)/20-13-0724;c3d 20-13-0724_labels.nii.gz  -binarize -o  20-13-0724_mask.nii.gz
	cd $(WORKDIR)/20-13-0724;../../createFeatureImagesOvary.sh -d 3 -x 20-13-0724_mask.nii.gz -l3 -n pre -a 20-13-0724_grey.nii.gz -f 0x2 -o ./20-13-0724-textfeat.nii.gz -r 1 -r 3 -s 2 -b 4
job22-13-0762:
	cd $(WORKDIR)/22-13-0762;c3d 22-13-0762_grey.nii.gz 22-13-0762_labels.nii.gz -copy-transform -o 22-13-0762_labels.nii.gz
	cd $(WORKDIR)/22-13-0762;c3d 22-13-0762_grey.nii.gz -orient RAI -o 22-13-0762_grey.nii.gz
	cd $(WORKDIR)/22-13-0762;c3d 22-13-0762_labels.nii.gz -orient RAI -o 22-13-0762_labels.nii.gz
	cd $(WORKDIR)/22-13-0762;c3d 22-13-0762_labels.nii.gz  -binarize -o  22-13-0762_mask.nii.gz
	cd $(WORKDIR)/22-13-0762;../../createFeatureImagesOvary.sh -d 3 -x 22-13-0762_mask.nii.gz -l3 -n pre -a 22-13-0762_grey.nii.gz -f 0x2 -o ./22-13-0762-textfeat.nii.gz -r 1 -r 3 -s 2 -b 4
job25-13-0794:
	cd $(WORKDIR)/25-13-0794;c3d 25-13-0794_grey.nii.gz 25-13-0794_labels.nii.gz -copy-transform -o 25-13-0794_labels.nii.gz
	cd $(WORKDIR)/25-13-0794;c3d 25-13-0794_grey.nii.gz -orient RAI -o 25-13-0794_grey.nii.gz
	cd $(WORKDIR)/25-13-0794;c3d 25-13-0794_labels.nii.gz -orient RAI -o 25-13-0794_labels.nii.gz
	cd $(WORKDIR)/25-13-0794;c3d 25-13-0794_labels.nii.gz  -binarize -o  25-13-0794_mask.nii.gz
	cd $(WORKDIR)/25-13-0794;../../createFeatureImagesOvary.sh -d 3 -x 25-13-0794_mask.nii.gz -l3 -n pre -a 25-13-0794_grey.nii.gz -f 0x2 -o ./25-13-0794-textfeat.nii.gz -r 1 -r 3 -s 2 -b 4
job27-13-0797:
	cd $(WORKDIR)/27-13-0797;c3d 27-13-0797_grey.nii.gz 27-13-0797_labels.nii.gz -copy-transform -o 27-13-0797_labels.nii.gz
	cd $(WORKDIR)/27-13-0797;c3d 27-13-0797_grey.nii.gz -orient RAI -o 27-13-0797_grey.nii.gz
	cd $(WORKDIR)/27-13-0797;c3d 27-13-0797_labels.nii.gz -orient RAI -o 27-13-0797_labels.nii.gz
	cd $(WORKDIR)/27-13-0797;c3d 27-13-0797_labels.nii.gz  -binarize -o  27-13-0797_mask.nii.gz
	cd $(WORKDIR)/27-13-0797;../../createFeatureImagesOvary.sh -d 3 -x 27-13-0797_mask.nii.gz -l3 -n pre -a 27-13-0797_grey.nii.gz -f 0x2 -o ./27-13-0797-textfeat.nii.gz -r 1 -r 3 -s 2 -b 4