Added vertebral labeling and warping of segs

shimming-toolbox · Dec 23, 2023 · 10251de · 10251de
1 parent b39f85e
commit 10251de
Showing 1 changed file with 54 additions and 2 deletions.
diff --git a/data_processing.ipynb b/data_processing.ipynb
@@ -136,9 +136,24 @@
    "id": "aac9d889",
    "metadata": {},
    "source": [
-    "## Verify quality control (QC) report\n",
+    "## Verify QC report (GRE segmentation)\n",
     "\n",
-    "Open the QC report located under `ds004906/qc/index.html`. Make sure the segmentations and registrations are correct before resuming the analysis."
+    "Open the quality control (QC) report located under `ds004906/qc/index.html`. Make sure the spinal cord segmentations are correct before resuming the analysis."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "34fd14bc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Label vertebrae on GRE scan\n",
+    "\n",
+    "# Given the low resolution of the GRE scan, the automatic detection of C2-C3 disc is unreliable. Therefore we need to use the manual disc labels that are part of the dataset.\n",
+    "for subject in subjects:\n",
+    "    os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
+    "#     !sct_label_vertebrae -i {subject}_acq-CoV_T2starw.nii.gz -s {subject}_acq-CoV_T2starw_seg.nii.gz -c t2 -initz -qc {path_qc}"
    ]
   },
   {
@@ -170,6 +185,43 @@
     "    for shim_mode in shim_modes:\n",
     "        !sct_register_multimodal -i {subject}_acq-anat{shim_mode}_TB1TFL.nii.gz -d ../anat/{subject}_acq-CoV_T2starw_crop.nii.gz -dseg ../anat/{subject}_acq-CoV_T2starw_crop_seg.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -qc {path_qc}"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4952bdfa",
+   "metadata": {},
+   "source": [
+    "## Verify QC report (B1maps to GRE registration)\n",
+    "\n",
+    "Open the QC report located under `ds004906/qc/index.html`. Make sure the registration are correct before resuming the analysis."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5fb3101a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Warping spinal cord segmentation to each B1 map\n",
+    "\n",
+    "for subject in subjects:\n",
+    "    os.chdir(os.path.join(path_data, subject, \"fmap\"))\n",
+    "    for shim_mode in shim_modes:\n",
+    "        !sct_apply_transfo -i ../anat/{subject}_acq-CoV_T2starw_crop_seg.nii.gz -d {subject}_acq-anat{shim_mode}_TB1TFL.nii.gz -w warp_{subject}_acq-CoV_T2starw_crop2{subject}_acq-anat{shim_mode}_TB1TFL.nii.gz -x linear"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f476b7ac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Extract B1+ value along the spinal cord\n",
+    "\n",
+    "# TODO"
+   ]
   }
  ],
  "metadata": {