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Copy pathUTAP_erode_HD_masks.sh
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UTAP_erode_HD_masks.sh
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#!/bin/bash
# Erode the brain masks
# mkdir ERODE
#
fslmaths MASK/Mask_AntCom_mask_R_Painted.nii.gz -ero ERODE/Mask_AntCom_mask_R_Painted.nii.gz
fslmaths MASK/Mask_AntCom_mask_L_Painted.nii.gz -ero ERODE/Mask_AntCom_mask_L_Painted.nii.gz
fslmaths MASK/Mask_Caudate_mask_L_Painted.nii.gz -ero ERODE/Mask_Caudate_mask_L_Painted.nii.gz
fslmaths MASK/Mask_Caudate_mask_R_Painted.nii.gz -ero ERODE/Mask_Caudate_mask_R_Painted.nii.gz
fslmaths MASK/Mask_GPe_mask_L_Painted.nii.gz -ero ERODE/Mask_GPe_mask_L_Painted.nii.gz
fslmaths MASK/Mask_GPe_mask_R_Painted.nii.gz -ero ERODE/Mask_GPe_mask_R_Painted.nii.gz
fslmaths MASK/Mask_GPi_mask_L_Painted.nii.gz -ero ERODE/Mask_GPi_mask_L_Painted.nii.gz
fslmaths MASK/Mask_GPi_mask_R_Painted.nii.gz -ero ERODE/Mask_GPi_mask_R_Painted.nii.gz
fslmaths MASK/Mask_IntCap_mask_L_Painted.nii.gz -ero ERODE/Mask_IntCap_mask_L_Painted.nii.gz
fslmaths MASK/Mask_IntCap_mask_R_Painted.nii.gz -ero ERODE/Mask_IntCap_mask_R_Painted.nii.gz
fslmaths MASK/Mask_IntThalAdh_mask_L_Painted.nii.gz -ero ERODE/Mask_IntThalAdh_mask_L_Painted.nii.gz
fslmaths MASK/Mask_IntThalAdh_mask_R_Painted.nii.gz -ero ERODE/Mask_IntThalAdh_mask_R_Painted.nii.gz
fslmaths MASK/Mask_LocCoer_mask_L_Painted.nii.gz -ero ERODE/Mask_LocCoer_mask_L_Painted.nii.gz
fslmaths MASK/Mask_LocCoer_mask_R_Painted.nii.gz -ero ERODE/Mask_LocCoer_mask_R_Painted.nii.gz
fslmaths MASK/Mask_Putamen_mask_L_Painted.nii.gz -ero ERODE/Mask_Putamen_mask_L_Painted.nii.gz
fslmaths MASK/Mask_Putamen_mask_R_Painted.nii.gz -ero ERODE/Mask_Putamen_mask_R_Painted.nii.gz
fslmaths MASK/Mask_RedNucl_mask_L_Painted.nii.gz -ero ERODE/Mask_RedNucl_mask_L_Painted.nii.gz
fslmaths MASK/Mask_RedNucl_mask_R_Painted.nii.gz -ero ERODE/Mask_RedNucl_mask_R_Painted.nii.gz
fslmaths MASK/Mask_STN_mask_L_Painted.nii.gz -ero ERODE/Mask_STN_mask_L_Painted.nii.gz
fslmaths MASK/Mask_STN_mask_R_Painted.nii.gz -ero ERODE/Mask_STN_mask_R_Painted.nii.gz
fslmaths MASK/Mask_SubLentIntCap_mask_L_Painted.nii.gz -ero ERODE/Mask_SubLentIntCap_mask_L_Painted.nii.gz
fslmaths MASK/Mask_SubLentIntCap_mask_R_Painted.nii.gz -ero ERODE/Mask_SubLentIntCap_mask_R_Painted.nii.gz
fslmaths MASK/Mask_SubNig_mask_L_Painted.nii.gz -ero ERODE/Mask_SubNig_mask_L_Painted.nii.gz
fslmaths MASK/Mask_SubNig_mask_R_Painted.nii.gz -ero ERODE/Mask_SubNig_mask_R_Painted.nii.gz
fslmaths MASK/Mask_Thalamus_mask_L_Painted.nii.gz -ero ERODE/Mask_Thalamus_mask_L_Painted.nii.gz
fslmaths MASK/Mask_Thalamus_mask_R_Painted.nii.gz -ero ERODE/Mask_Thalamus_mask_R_Painted.nii.gz
mrconvert ERODE/Mask_AntCom_mask_R_Painted.nii.gz ERODE/Mask_AntCom_mask_R_Painted.mif
mrconvert ERODE/Mask_AntCom_mask_L_Painted.nii.gz ERODE/Mask_AntCom_mask_L_Painted.mif
mrconvert ERODE/Mask_Caudate_mask_L_Painted.nii.gz ERODE/Mask_Caudate_mask_L_Painted.mif
mrconvert ERODE/Mask_Caudate_mask_R_Painted.nii.gz ERODE/Mask_Caudate_mask_R_Painted.mif
mrconvert ERODE/Mask_GPe_mask_L_Painted.nii.gz ERODE/Mask_GPe_mask_L_Painted.mif
mrconvert ERODE/Mask_GPe_mask_R_Painted.nii.gz ERODE/Mask_GPe_mask_R_Painted.mif
mrconvert ERODE/Mask_GPi_mask_L_Painted.nii.gz ERODE/Mask_GPi_mask_L_Painted.mif
mrconvert ERODE/Mask_GPi_mask_R_Painted.nii.gz ERODE/Mask_GPi_mask_R_Painted.mif
mrconvert ERODE/Mask_IntCap_mask_L_Painted.nii.gz ERODE/Mask_IntCap_mask_L_Painted.mif
mrconvert ERODE/Mask_IntCap_mask_R_Painted.nii.gz ERODE/Mask_IntCap_mask_R_Painted.mif
mrconvert ERODE/Mask_IntThalAdh_mask_L_Painted.nii.gz ERODE/Mask_IntThalAdh_mask_L_Painted.mif
mrconvert ERODE/Mask_IntThalAdh_mask_R_Painted.nii.gz ERODE/Mask_IntThalAdh_mask_R_Painted.mif
mrconvert ERODE/Mask_LocCoer_mask_L_Painted.nii.gz ERODE/Mask_LocCoer_mask_L_Painted.mif
mrconvert ERODE/Mask_LocCoer_mask_R_Painted.nii.gz ERODE/Mask_LocCoer_mask_R_Painted.mif
mrconvert ERODE/Mask_Putamen_mask_L_Painted.nii.gz ERODE/Mask_Putamen_mask_L_Painted.mif
mrconvert ERODE/Mask_Putamen_mask_R_Painted.nii.gz ERODE/Mask_Putamen_mask_R_Painted.mif
mrconvert ERODE/Mask_RedNucl_mask_L_Painted.nii.gz ERODE/Mask_RedNucl_mask_L_Painted.mif
mrconvert ERODE/Mask_RedNucl_mask_R_Painted.nii.gz ERODE/Mask_RedNucl_mask_R_Painted.mif
mrconvert ERODE/Mask_STN_mask_L_Painted.nii.gz ERODE/Mask_STN_mask_L_Painted.mif
mrconvert ERODE/Mask_STN_mask_R_Painted.nii.gz ERODE/Mask_STN_mask_R_Painted.mif
mrconvert ERODE/Mask_SubLentIntCap_mask_L_Painted.nii.gz ERODE/Mask_SubLentIntCap_mask_L_Painted.mif
mrconvert ERODE/Mask_SubLentIntCap_mask_R_Painted.nii.gz ERODE/Mask_SubLentIntCap_mask_R_Painted.mif
mrconvert ERODE/Mask_SubNig_mask_L_Painted.nii.gz ERODE/Mask_SubNig_mask_L_Painted.mif
mrconvert ERODE/Mask_SubNig_mask_R_Painted.nii.gz ERODE/Mask_SubNig_mask_R_Painted.mif
mrconvert ERODE/Mask_Thalamus_mask_L_Painted.nii.gz ERODE/Mask_Thalamus_mask_L_Painted.mif
mrconvert ERODE/Mask_Thalamus_mask_R_Painted.nii.gz ERODE/Mask_Thalamus_mask_R_Painted.mif