From 84ba26feb1c2094e956cc43d808bd857d156d934 Mon Sep 17 00:00:00 2001
From: jcohenadad <jcohen@polymtl.ca>
Date: Thu, 4 Jul 2024 16:07:51 -0400
Subject: [PATCH] Use cropped data for DWI processing

Addresses #46
---
 batch_processing.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/batch_processing.sh b/batch_processing.sh
index 9996c33..588d242 100644
--- a/batch_processing.sh
+++ b/batch_processing.sh
@@ -273,6 +273,7 @@ for file_dwi in "${files_dwi[@]}"; do
   file_dwi_seg="${FILESEG}"
   # Crop data for faster processing
   sct_crop_image -i "${file_dwi}".nii.gz -m "${file_dwi_seg}".nii.gz -dilate 15x15x0 -o "${file_dwi}"_crop.nii.gz
+  file_dwi=${file_dwi}_crop
   # Motion correction
   sct_dmri_moco -i ${file_dwi}.nii.gz -bvec ${file_bvec} -x spline
   file_dwi=${file_dwi}_moco