From a6d684c8365ebf79908d37586ca45c20c60f89f2 Mon Sep 17 00:00:00 2001
From: Kalum Ost <43527660+SomeoneInParticular@users.noreply.github.com>
Date: Thu, 28 Nov 2024 18:48:01 -0500
Subject: [PATCH] batch_single_subject.sh: Added missing second-pass
 segmentation using smoothed SC

---
 single_subject/batch_single_subject.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh
index 525af85..40e2890 100755
--- a/single_subject/batch_single_subject.sh
+++ b/single_subject/batch_single_subject.sh
@@ -402,6 +402,9 @@ sct_deepseg -task seg_sc_contrast_agnostic -i t1.nii.gz
 sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz
 # Tips: use flag "-sigma" to specify smoothing kernel size (in mm)
 
+# Second-pass segmentation using the smoothed anatomical image
+sct_deepseg_sc -i t1_smooth.nii.gz -c t1 -qc ~/qc_singleSubj
+
 # Align the spinal cord in the right-left direction using slice-wise translations.
 sct_flatten_sagittal -i t1.nii.gz -s t1_seg.nii.gz
 # Note: Use for visualization purposes only