Use SCT segmentation, and only on CoV GRE scan

Why doing it on all scans?

Analysis.ipynb

@@ -58,12 +58,12 @@
     "import subprocess\n",
     "import glob\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "from PIL import Image\n",
-    "from IPython.display import display\n",
-    "from tabulate import tabulate\n",
+    "# import matplotlib.pyplot as plt\n",
+    "# from PIL import Image\n",
+    "# from IPython.display import display\n",
+    "# from tabulate import tabulate\n",
     "import nibabel as nib\n",
-    "import pandas as pd"
+    "# import pandas as pd"
    ]
   },
   {
@@ -77,7 +77,24 @@
     "\n",
     "!datalad install https://github.com/OpenNeuroDatasets/ds004906.git\n",
     "os.chdir(\"ds004906\")\n",
-    "!datalad get sub-01/"
+    "# !datalad get . # uncomment for production\n",
+    "!datalad get sub-01/  # comment for debugging\n",
+    "path_data = os.getcwd()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e95d87a4-3194-4369-b6cb-933ad1d5cfa3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Run segmentation on GRE scan\n",
+    "\n",
+    "subjects = glob.glob(\"sub-*\")\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 {os.path.join(path_data, \"qc\")}"
    ]
   },
   {
@@ -491,21 +508,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Run GRE segmentation\n",
-    "path_data = './RF_shimming_project_cleanupload'\n",
-    "path_data_abs = os.path.abspath(path_data)\n",
-    "shimcasenames=['noshim','patspec','volspec','phaseonly','cvred','target','sareff']\n",
-    "\n",
-    "# Loop across subjects\n",
-    "for entry in os.scandir(folder_path):\n",
-    "    if entry.is_dir():\n",
-    "        subject=entry.name\n",
-    "        # Loop across shim cases\n",
-    "        for shimcase in range(len(shimcasenames)):\n",
-    "            print(f\"Running segmentation for: subject={subject}, shimcase={shimcase}\")\n",
-    "            os.chdir(os.path.join(path_data_abs, subject, shimcase))\n",
-    "            GRE_segment_monai(subjectpath,shimcasenames[shimcase])\n",
-    "            #B1_map_process(subjectpath,shimcasenames[shimcase])"
+    "# # Run GRE segmentation\n",
+    "# path_data = './RF_shimming_project_cleanupload'\n",
+    "# path_data_abs = os.path.abspath(path_data)\n",
+    "# shimcasenames=['noshim','patspec','volspec','phaseonly','cvred','target','sareff']\n",
+    "\n",
+    "# # Loop across subjects\n",
+    "# for entry in os.scandir(folder_path):\n",
+    "#     if entry.is_dir():\n",
+    "#         subject=entry.name\n",
+    "#         # Loop across shim cases\n",
+    "#         for shimcase in range(len(shimcasenames)):\n",
+    "#             print(f\"Running segmentation for: subject={subject}, shimcase={shimcase}\")\n",
+    "#             os.chdir(os.path.join(path_data_abs, subject, shimcase))\n",
+    "#             GRE_segment_monai(subjectpath,shimcasenames[shimcase])\n",
+    "#             #B1_map_process(subjectpath,shimcasenames[shimcase])"
    ]
   },
   {