From ab9cad8cd09051dd6d2fb08bfe2c9c9dd5ad9e9b Mon Sep 17 00:00:00 2001 From: Michiel Cottaar Date: Wed, 25 Sep 2019 10:01:47 +0100 Subject: [PATCH] BUG: added extensions to filenames for wb_command --- DiffusionPreprocessing/scripts/DiffusionToStructural.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DiffusionPreprocessing/scripts/DiffusionToStructural.sh b/DiffusionPreprocessing/scripts/DiffusionToStructural.sh index 2aa058bfe..eda85b204 100755 --- a/DiffusionPreprocessing/scripts/DiffusionToStructural.sh +++ b/DiffusionPreprocessing/scripts/DiffusionToStructural.sh @@ -103,7 +103,7 @@ DILATE_DISTANCE=echo "$DiffRes * 12" # Extrapolates the diffusion data up to 12 if [ ${GdcorrectionFlag} -eq 1 ]; then echo "Correcting Diffusion data for gradient nonlinearities and registering to structural space" ${FSLDIR}/bin/convertwarp --rel --relout --warp1="$DataDirectory"/warped/fullWarp --postmat="$WorkingDirectory"/diff2str.mat --ref="$T1wRestoreImage"_${DiffRes} --out="$WorkingDirectory"/grad_unwarp_diff2str - ${CARET7DIR}/wb_command -volume-dilate $DataDirectory/warped/data_warped $DILATE_DISTANCE NEAREST $DataDirectory/warped/data_warped_dilated + ${CARET7DIR}/wb_command -volume-dilate $DataDirectory/warped/data_warped.nii.gz $DILATE_DISTANCE NEAREST $DataDirectory/warped/data_warped_dilated.nii.gz ${FSLDIR}/bin/applywarp --rel -i "$DataDirectory"/warped/data_warped_dilated -r "$T1wRestoreImage"_${DiffRes} -w "$WorkingDirectory"/grad_unwarp_diff2str --interp=spline -o "$T1wOutputDirectory"/data #Create a mask covering voxels within the field of view for all volumes @@ -116,7 +116,7 @@ if [ ${GdcorrectionFlag} -eq 1 ]; then ${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/grad_dev -mas "$T1wOutputDirectory"/nodif_brain_mask_temp "$T1wOutputDirectory"/grad_dev #Mask-out values outside the brain else #Register diffusion data to T1w space without considering gradient nonlinearities - ${CARET7DIR}/wb_command -volume-dilate $DataDirectory/data $DILATE_DISTANCE NEAREST $DataDirectory/data_dilated + ${CARET7DIR}/wb_command -volume-dilate $DataDirectory/data.nii.gz $DILATE_DISTANCE NEAREST $DataDirectory/data_dilated.nii.gz ${FSLDIR}/bin/flirt -in "$DataDirectory"/data_dilated -ref "$T1wRestoreImage"_${DiffRes} -applyxfm -init "$WorkingDirectory"/diff2str.mat -interp spline -out "$T1wOutputDirectory"/data #Create a mask covering voxels within the field of view for all volumes