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malfCommand.sh
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malfCommand.sh
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inputPath=${PWD}/
${ANTSPATH}/antsJointLabelFusion.sh \
-d 2 \
-c 2 -j 4 \
-x or \
-o ${inputPath}/Output/example \
-p ${inputPath}/Output/examplePosteriors%02d.nii.gz \
-t ${inputPath}/T_template0.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-10_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-10_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-11_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-11_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-12_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-12_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-13_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-13_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-14_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-14_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-15_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-15_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-16_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-16_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-17_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-17_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-18_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-18_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-19_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-19_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-1_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-1_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-20_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-20_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-2_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-2_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-3_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-3_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-4_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-4_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-5_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-5_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-6_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-6_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-7_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-7_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-8_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-8_DKT31_CMA_labels_slice118.nii.gz \
-g ${inputPath}/Atlases/OASIS-TRT-20-9_slice118.nii.gz -l ${inputPath}/Labels/OASIS-TRT-20-9_DKT31_CMA_labels_slice118.nii.gz \