DEBUG: Debug SynthStrip

Author: jhlegarreta

.github/workflows/notebooks.yml

@@ -69,6 +69,8 @@ jobs:
       - name: Download SynthStrip model
         run: |
           wget https://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/synthstrip/models/synthstrip.1.pt -P "${TEST_DATA_HOME}"
+          echo "Test data home"
+          tree ${TEST_DATA_HOME}
 
       - name: Install TeX Live
         run: |

docs/notebooks/bold_realignment.ipynb

@@ -74,12 +74,25 @@
     "    bmask_path = (\n",
     "        OUTPUT_DIR / bold_run.parent / f\"{bold_run.name.rsplit('_', 1)[0]}_label-brain_mask.nii.gz\"\n",
     "    )\n",
+    "    print(f\"Data path: {DATA_PATH}\")\n",
+    "    for item in DATA_PATH.iterdir():\n",
+    "        print(f\"Item: {item}\")\n",
+    "\n",
+    "    if not DATA_PATH.exists() or not DATA_PATH.is_dir():\n",
+    "        raise FileNotFoundError(f\"Directory does not exist: {DATA_PATH}\")\n",
+    "\n",
+    "    _path = DATA_PATH / \"synthstrip.1.pt\"\n",
+    "    if not _path.exists() or not _path.is_dir():\n",
+    "        raise FileNotFoundError(f\"synthstrip file does not exist: {_path}\")\n",
+    "\n",
     "    if not bmask_path.exists():\n",
     "        bmsk_results = SynthStrip(\n",
     "            in_file=str(avg_path),\n",
     "            use_gpu=True,\n",
-    "            model=DATA_PATH / \"synthstrip.1.pt\",\n",
+    "            model=str(DATA_PATH / \"synthstrip.1.pt\"),\n",
     "        ).run(cwd=str(WORKDIR))\n",
+    "        print(f\"Outputs: {bmsk_results.outputs}\")\n",
+    "        print(f\"Out_mask: {bmsk_results.outputs.out_mask}\")\n",
     "        copy(bmsk_results.outputs.out_mask, bmask_path)\n",
     "\n",
     "    dilmask_path = (\n",