Replaced sct_label_vertebrae with sct_label_utils

Thank you @valosekj :) Context: spinalcordtoolbox/spinalcordtoolbox#4323
shimming-toolbox · Dec 23, 2023 · 7e9b051 · 7e9b051
1 parent 3c56ddb
commit 7e9b051
Showing 1 changed file with 16 additions and 22 deletions.
diff --git a/data_processing.ipynb b/data_processing.ipynb
@@ -101,8 +101,10 @@
     "\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/  # debugging\n",
+    "# Get derivatives containing manual labels\n",
+    "!datalad get derivatives"
    ]
   },
   {
@@ -116,7 +118,8 @@
     "\n",
     "path_data = os.getcwd()\n",
     "path_qc = os.path.join(path_data, \"qc\")\n",
-    "shim_modes = [\"CP\", \"CoV\", \"patient\", \"phase\", \"SAReff\", \"target\", \"volume\"]\n",
+    "# shim_modes = [\"CP\", \"CoV\", \"patient\", \"phase\", \"SAReff\", \"target\", \"volume\"]\n",
+    "shim_modes = [\"CP\", \"CoV\"]  # debugging\n",
     "subjects = glob.glob(\"sub-*\")"
    ]
   },
@@ -147,11 +150,16 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "95cafe0d",
+   "id": "862dc562",
    "metadata": {},
    "outputs": [],
    "source": [
-    "os.path.join(path_data, \"derivatives\", \"labels\", subject, \"anat\", f\"{subject}_acq-CoV_T2starw_label-discs_dseg.nii.gz\")\n"
+    "# Crop GRE scan for faster processing and better registration results\n",
+    "\n",
+    "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"
    ]
   },
   {
@@ -167,23 +175,9 @@
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
     "    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}"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "862dc562",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Crop GRE scan for faster processing and better registration results\n",
-    "\n",
-    "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\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    "
+    "    !sct_label_utils -i {subject}_acq-CoV_T2starw_crop_seg.nii.gz -disc {fname_label_discs} -o {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz\n",
+    "    # Generate QC report to assess labeled segmentation\n",
+    "    !sct_qc -i {subject}_acq-CoV_T2starw_crop.nii.gz -s {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -p sct_label_vertebrae -qc {path_qc} -qc-subject {subject}"
    ]
   },
   {