From 61f67c3fb7007c8dd26d16ae37d897c18de30f99 Mon Sep 17 00:00:00 2001
From: jcohenadad <jcohen@polymtl.ca>
Date: Wed, 17 Jan 2024 14:51:44 -0500
Subject: [PATCH] Replacing slicereg by deep learning registration

Fixes #35
---
 data_processing.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data_processing.ipynb b/data_processing.ipynb
index c5fb73a..e957549 100644
--- a/data_processing.ipynb
+++ b/data_processing.ipynb
@@ -260,7 +260,7 @@
     "    for shim_mode in shim_modes:\n",
     "        # Don't do it for CoV_T2starw\n",
     "        if shim_mode != 'CoV':\n",
-    "            !sct_register_multimodal -i {subject}_acq-{shim_mode}_T2starw.nii.gz -d {subject}_acq-CoV_T2starw_crop.nii.gz -dseg {subject}_acq-CoV_T2starw_crop_seg.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -qc {path_qc}"
+    "            !sct_register_multimodal -i {subject}_acq-{shim_mode}_T2starw.nii.gz -d {subject}_acq-CoV_T2starw_crop.nii.gz -dseg {subject}_acq-CoV_T2starw_crop_seg.nii.gz -param step=1,type=im,algo=dl -qc {path_qc}"
    ]
   },
   {