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

Do not remove fMRI 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. 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.

Author: jhlegarreta

.github/workflows/notebooks.yml

@@ -41,12 +41,35 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - 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: Download data from OSF
         run: |
           mkdir ${TEST_DATA_HOME}
           pip install osfclient
           osf -p 39k4x fetch hcpdata.npz "${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 TeX Live
         run: |
           sudo apt-get update

docs/notebooks/bold_realignment.ipynb

@@ -78,6 +78,7 @@
     "        bmsk_results = SynthStrip(\n",
     "            in_file=str(avg_path),\n",
     "            use_gpu=True,\n",
+    "            model=DATA_PATH / \"synthstrip.1.pt\",\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))