From ecaf0aa1f1a31af9be85d9fa72b8ef2bf02a7b89 Mon Sep 17 00:00:00 2001 From: tomaroberts Date: Fri, 12 Nov 2021 13:06:09 +0000 Subject: [PATCH] Adds in-plane isotropic padding of SVR-output.nii.gz --- scripts/docker-recon-brain-auto.bash | 3 +++ 1 file changed, 3 insertions(+) diff --git a/scripts/docker-recon-brain-auto.bash b/scripts/docker-recon-brain-auto.bash index 4ad994b..91ebc81 100755 --- a/scripts/docker-recon-brain-auto.bash +++ b/scripts/docker-recon-brain-auto.bash @@ -467,6 +467,9 @@ if [[ -f ${test_file} ]];then # TAR - rename files mv ${main_dir}/${roi_recon[${selected_recon_roi}]}-output.nii.gz ${main_dir}/${roi_recon[${selected_recon_roi}]}-output-withoutReorientation.nii.gz cp ${main_dir}/reo-${roi_recon[${selected_recon_roi}]}-output.nii.gz ${main_dir}/${roi_recon[${selected_recon_roi}]}-output.nii.gz + + # TAR - pad in-plane so square FOV + ${mirtk_path}/mirtk resample-to-iso-grid ${main_dir}/${roi_recon[${selected_recon_roi}]}-output.nii.gz ${main_dir}/${roi_recon[${selected_recon_roi}]}-output.nii.gz 2 # TAR - move final files to /recon dir cp ${main_dir}/${roi_recon[${selected_recon_roi}]}-output-withoutReorientation.nii.gz ${default_recon_dir}/${roi_recon[${selected_recon_roi}]}-output-withoutReorientation.nii.gz