Use another segmentation method for sub-04 (#32)

shimming-toolbox · Jan 9, 2024 · 65dbd7a · 65dbd7a
1 parent cd5d649
commit 65dbd7a
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/data_processing.ipynb b/data_processing.ipynb
@@ -139,7 +139,11 @@
     "\n",
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
-    "    !sct_deepseg_sc -i {subject}_acq-CoV_T2starw.nii.gz -c t2 -qc {path_qc}"
+    "    # Use another syntax for sub-04. See: https://github.com/shimming-toolbox/rf-shimming-7t/issues/31\n",
+    "    if subject == 'sub-04':\n",
+    "        !sct_deepseg_sc -i {subject}_acq-CoV_T2starw.nii.gz -c t2 -qc {path_qc}\n",
+    "    else:\n",
+    "        !sct_deepseg_sc -i {subject}_acq-CoV_T2starw.nii.gz -c t2s -qc {path_qc}"
    ]
   },
   {
@@ -386,7 +390,6 @@
     "    ax.set_xticklabels([''] * len(original_vector))\n",
     "\n",
     "    ax.set_title(f'{subject}')\n",
-    "#     ax.set_xlabel('Normalized Index')\n",
     "    ax.set_ylabel('B1+ efficiency [nT/V]')\n",
     "\n",
     "    # Add legend only to the first subplot\n",