TST: Do not remove fMRI BOLD notebook from list of discovered notebooks

Do not remove fMRI BOLD realignment notebook from list of discovered
notebooks: this will allow running the notebook at the time scheduled by
the `notebooks.yml` GHA workflow file.

Download `SynthStrip` model for skull stripping. `SynthStrip` is used by
the fMRI BOLD realignment notebook.

Fixes:
```
FileNotFoundError                         Traceback (most recent call last)
Cell In[4], line 19
     14 if not bmask_path.exists():
     15     bmsk_results = SynthStrip(
     16         in_file=str(avg_path),
     17         use_gpu=True,
     18     ).run(cwd=str(WORKDIR))
---> 19     copy(bmsk_results.outputs.out_mask,bmask_path)

(...)

FileNotFoundError: [Errno 2] No such file or directory:
 '/home/runner/tmp/nifreezedev/ismrm25/sub-01_task-mixedgamblestask_run-03_boldref_desc-brain_mask.nii.gz'
```

raised for example at:
https://github.com/jhlegarreta/nifreeze/actions/runs/14897027210/job/41841440531#step:11:102

Modify the call to the `SynthStrip` workflow in the notebook so that the
model is loaded from a file that is provided as an argument.

Install AFNI in the GHA workflow.

Check if `CUDA` is available in the GHA workflow file and set an
environment variable to run the `SynthStrip` process on CPU if not
available.

Author: jhlegarreta

.github/workflows/notebooks.yml

@@ -41,6 +41,33 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Check for nvcc and set CUDA flag
+        id: detect-cuda
+        run: |
+          if command -v nvcc &> /dev/null; then
+            echo "nvcc found: CUDA is available"
+            echo "HAS_CUDA=true" >> $GITHUB_ENV
+          else
+            echo "nvcc not found: CUDA is not available"
+            echo "HAS_CUDA=false" >> $GITHUB_ENV
+          fi
+
+      - name: Install AFNI
+        run: |
+          # Detect Ubuntu version
+          UBUNTU_VERSION=$(lsb_release -rs | cut -d. -f1)
+          AFNI_PACKAGE="linux_ubuntu_${UBUNTU_VERSION}_64"
+          echo "Detected Ubuntu version: $UBUNTU_VERSION"
+          echo "Using AFNI package: $AFNI_PACKAGE"
+          # Install dependencies
+          sudo apt-get update
+          sudo apt-get install -y tcsh curl libglu1-mesa libxmu6 libxm4 libgsl-dev libglw1-mesa
+          # Download and install AFNI
+          curl -O https://afni.nimh.nih.gov/pub/dist/bin/${AFNI_PACKAGE}/@update.afni.binaries
+          tcsh @update.afni.binaries -package $AFNI_PACKAGE -do_extras
+          # Add AFNI to PATH
+          echo "$HOME/abin" >> $GITHUB_PATH
+
       - name: Install TeX Live
         run: |
           sudo apt-get update
@@ -69,6 +96,10 @@ jobs:
           pip install osfclient
           osf -p 39k4x fetch hcpdata.npz "${TEST_DATA_HOME}/hcpdata.npz"
 
+      - name: Download SynthStrip model
+        run: |
+          wget https://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/synthstrip/models/synthstrip.1.pt -P "${TEST_DATA_HOME}"
+
       - name: Install tox
         run: |
           python -m pip install --upgrade pip

docs/notebooks/bold_realignment.ipynb

@@ -74,10 +74,12 @@
     "    bmask_path = (\n",
     "        OUTPUT_DIR / bold_run.parent / f\"{bold_run.name.rsplit('_', 1)[0]}_label-brain_mask.nii.gz\"\n",
     "    )\n",
+    "    use_gpu = getenv(\"HAS_CUDA\", \"false\").lower() == \"true\"\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",
+    "            use_gpu=use_gpu,\n",
     "        ).run(cwd=str(WORKDIR))\n",
     "        copy(bmsk_results.outputs.out_mask, bmask_path)\n",
     "\n",

tools/run_notebooks.py

@@ -27,8 +27,5 @@
 
 # Find and run the notebooks
 notebooks = glob.glob("docs/notebooks/*.ipynb")
-# Make bold_realignment.ipynb Jupyter notebook an exception as it involves running a realignment
-# process for several DataLad datasets, which requires long running times.
-notebooks.remove("docs/notebooks/bold_realignment.ipynb")
 
 sys.exit(subprocess.call(["pytest", "--nbmake"] + notebooks))