Warping vertebral levels

shimming-toolbox · Dec 23, 2023 · 5fdcfa9 · 5fdcfa9
1 parent 10251de
commit 5fdcfa9
Showing 1 changed file with 33 additions and 17 deletions.
diff --git a/data_processing.ipynb b/data_processing.ipynb
@@ -56,12 +56,15 @@
     "\n",
     "For each subject:\n",
     "\n",
-    "- Segment the SC from the GRE scan\n",
-    "- Extract the signal intensity within this mask from the GRE scans\n",
-    "- Coregister the TFL_B1map to the corresponding GRE scan from each subfolder (CVred, Noshim, etc.)\n",
-    "- Apply the computed warping field to bring the SC segmentation to the TFL_B1map\n",
-    "- Convert the B1+ maps to nT/V units\n",
-    "- Extract the B1+ value within the registered mask"
+    "- Segment the SC on GRE scan\n",
+    "- Label vertebral levels on GRE scan using existing manual disc labels\n",
+    "- Extract the signal intensity on the GRE scan within the spinal cord\n",
+    "- Register each B1 map (CP, CoV, etc.) to the GRE scan\n",
+    "- Apply the computed warping field to bring the segmentation and vertebral levels to the B1 map\n",
+    "- Convert the B1 map to nT/V units\n",
+    "- Extract the B1 map value within the spinal cord\n",
+    "\n",
+    "Slow processes are indicated with the emoji ⏳"
    ]
   },
   {
@@ -98,8 +101,8 @@
     "\n",
     "!datalad install https://github.com/OpenNeuroDatasets/ds004906.git\n",
     "os.chdir(\"ds004906\")\n",
-    "# !datalad get . # uncomment for production\n",
-    "!datalad get sub-01/  # comment for debugging"
+    "!datalad get . # uncomment for production\n",
+    "# !datalad get sub-01/  # comment for debugging"
    ]
   },
   {
@@ -144,7 +147,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34fd14bc",
+   "id": "ab6a7dbe",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "os.path.join(path_data, \"derivatives\", \"labels\", subject, \"anat\", f\"{subject}_acq-CoV_T2starw_label-discs_dseg.nii.gz\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4e1a6ae1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -153,7 +166,8 @@
     "# 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}"
+    "    fname_label_discs = os.path.join(path_data, \"derivatives\", \"labels\", subject, \"anat\", f\"{subject}_acq-CoV_T2starw_label-discs_dseg.nii.gz\")\n",
+    "    !sct_label_vertebrae -i {subject}_acq-CoV_T2starw.nii.gz -s {subject}_acq-CoV_T2starw_seg.nii.gz -c t2 -discfile {fname_label_discs} -qc {path_qc}"
    ]
   },
   {
@@ -168,7 +182,8 @@
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
     "    !sct_crop_image -i {subject}_acq-CoV_T2starw.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop.nii.gz\n",
-    "    !sct_crop_image -i {subject}_acq-CoV_T2starw_seg.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop_seg.nii.gz"
+    "    !sct_crop_image -i {subject}_acq-CoV_T2starw_seg.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop_seg.nii.gz\n",
+    "    !sct_crop_image -i {subject}_acq-CoV_T2starw_seg_labeled.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz    "
    ]
   },
   {
@@ -178,7 +193,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Register TFL B1maps to the GRE scan\n",
+    "# Register TFL B1maps to the GRE scan ⏳\n",
     "\n",
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"fmap\"))\n",
@@ -188,7 +203,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4952bdfa",
+   "id": "679f1193",
    "metadata": {},
    "source": [
     "## Verify QC report (B1maps to GRE registration)\n",
@@ -199,22 +214,23 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5fb3101a",
+   "id": "623c26cd",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Warping spinal cord segmentation to each B1 map\n",
+    "# Warping spinal cord segmentation and vertebral level 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"
+    "        !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 -o {subject}_acq-anat{shim_mode}_TB1TFL_seg.nii.gz\n",
+    "        !sct_apply_transfo -i ../anat/{subject}_acq-CoV_T2starw_crop_seg_labeled.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 nn -o {subject}_acq-anat{shim_mode}_TB1TFL_seg_labeled.nii.gz"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f476b7ac",
+   "id": "ef34c2a1",
    "metadata": {},
    "outputs": [],
    "source": [