From 7708ee252ec2c491f23fe01fda126152bf8087e6 Mon Sep 17 00:00:00 2001
From: Kalum Ost <43527660+SomeoneInParticular@users.noreply.github.com>
Date: Thu, 28 Nov 2024 17:07:17 -0500
Subject: [PATCH] Added missing `-vertfile` flag

---
 single_subject/batch_single_subject.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh
index 370caad..b7c7bee 100755
--- a/single_subject/batch_single_subject.sh
+++ b/single_subject/batch_single_subject.sh
@@ -77,7 +77,7 @@ sct_process_segmentation -i t2_seg.nii.gz -vert 3:4 -vertfile t2_seg_labeled.nii
 # Aggregate CSA value per level
 sct_process_segmentation -i t2_seg.nii.gz -vert 3:4 -vertfile t2_seg_labeled.nii.gz -perlevel 1 -o csa_perlevel.csv
 # Aggregate CSA value per slices
-sct_process_segmentation -i t2_seg.nii.gz -z 30:35 -perslice 1 -o csa_perslice.csv
+sct_process_segmentation -i t2_seg.nii.gz -z 30:35 -vertfile t2_seg_labeled.nii.gz -perslice 1 -o csa_perslice.csv
 
 # A drawback of vertebral level-based CSA is that it doesn’t consider neck flexion and extension.
 # To overcome this limitation, the CSA can instead be computed using the distance to a reference point.