From 3dd129975f946cc2e54b3c70780a02a68f121a1e Mon Sep 17 00:00:00 2001
From: jcohenadad <jcohen@polymtl.ca>
Date: Fri, 22 Dec 2023 17:15:12 -0500
Subject: [PATCH] Added registration code

---
 Analysis.ipynb | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/Analysis.ipynb b/Analysis.ipynb
index 30a744f..16d9795 100644
--- a/Analysis.ipynb
+++ b/Analysis.ipynb
@@ -97,6 +97,20 @@
     "    !sct_deepseg_sc -i {subject}_acq-CoV_T2starw.nii.gz -c t2 -qc {os.path.join(path_data, \"qc\")}"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "014af6ec",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Register TFL B1maps to the GRE scan\n",
+    "\n",
+    "for subject in subjects:\n",
+    "    os.chdir(os.path.join(path_data, subject, \"fmap\"))\n",
+    "    !sct_register_multimodal -i {subject}_acq-anatCoV_TB1TFL.nii.gz -d ../anat/{subject}_acq-CoV_T2starw.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -qc {os.path.join(path_data, \"qc\")}"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -749,7 +763,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.10.8"
   }
  },
  "nbformat": 4,