Add MNI atlas labeling notebook for AAL3 and Brodmann parcels

docs/examples/Makefile

@@ -29,6 +29,7 @@ EXAMPLE_NOTEBOOKS = getting_started_io/00_test_installation.ipynb \
 					head_models/46_precompute_fluence.ipynb \
 					head_models/48_headmodel_landmarks_verification.ipynb \
 					head_models/51_spring_relaxation_registration.ipynb \
+					head_models/52_mni_atlas_labels_aal3_brodmann.ipynb \
 					augmentation/61_synthetic_artifacts_example.ipynb \
 					augmentation/62_synthetic_hrfs_example.ipynb \
 					physio/71_ampd_heartbeat.ipynb \

src/cedalion/bibliography/references.bib

@@ -594,4 +594,25 @@ @article{Luke2025
   doi = {10.1038/s41597-024-04136-9},
 }
 
+@article{Rolls2020,
+	title = {Automated anatomical labelling atlas 3},
+	journal = {NeuroImage},
+	volume = {206},
+	pages = {116189},
+	year = {2020},
+	issn = {1053-8119},
+	doi = {https://doi.org/10.1016/j.neuroimage.2019.116189},
+	author = {Edmund T. Rolls and Chu-Chung Huang and Ching-Po Lin and Jianfeng Feng and Marc Joliot},
+}
+
+@book{Mai2017,
+  title = {Human Brain in Standard {{MNI}} Space: Structure and Function: A Comprehensive Pocket Atlas},
+  shorttitle = {Human Brain in Standard {{MNI}} Space},
+  author = {Mai, J{\"u}rgen K. and Majtanik, Milan},
+  year = 2017,
+  publisher = {Academic Press, an imprint of Elsevier},
+  address = {London ; San Diego, CA},
+  isbn = {978-0-12-811275-5},
+  lccn = {RC386.6.M34 M347 2017},
+}
 

src/cedalion/data/__init__.py

@@ -101,6 +101,37 @@ def get(fname: str | Path) -> Path:
     return files("cedalion.data").joinpath(fname)
 
 
+@dataclass
+class AtlasFiles:
+    """Paths for a bundled atlas volume and label lookup."""
+
+    basedir: Path
+    nifti: Path
+    labels_json: Path
+
+
+def get_aal3_atlas_files() -> AtlasFiles:
+    """Return paths to the bundled AAL3 atlas volume and label lookup."""
+
+    atlas_dir = get("atlases/aal3")
+    return AtlasFiles(
+        basedir=atlas_dir,
+        nifti=atlas_dir / "ROI_MNI_V7_1mm.nii",
+        labels_json=atlas_dir / "aal_labels.json",
+    )
+
+
+def get_brodmann_atlas_files() -> AtlasFiles:
+    """Return paths to the bundled Brodmann atlas volume and label lookup."""
+
+    atlas_dir = get("atlases/brodmann")
+    return AtlasFiles(
+        basedir=atlas_dir,
+        nifti=atlas_dir / "Brodmann_Mai_Matajnik.nii",
+        labels_json=atlas_dir / "brodmann_labels.json",
+    )
+
+
 def get_ninja_cap_probe():
     """Load the fullhead Ninja NIRS cap probe."""
 
@@ -544,10 +575,12 @@ def get_atlas_files(atlas : str) -> tuple[Path, Path]:
         fnames = DATASETS.fetch("atlas_aal3.zip", processor=pooch.Unzip())
         fname_volume = [Path(i) for i in fnames if i.endswith(".nii")][0]
         fname_labels = [Path(i) for i in fnames if i.endswith(".json")][0]
+        cite("Rolls2020")
     elif atlas == "brodmann":
-        fnames = DATASETS.fetch("atlas_aal3.zip", processor=pooch.Unzip())
+        fnames = DATASETS.fetch("atlas_brodmann.zip", processor=pooch.Unzip())
         fname_volume = [Path(i) for i in fnames if i.endswith(".nii")][0]
         fname_labels = [Path(i) for i in fnames if i.endswith(".json")][0]
+        cite("Mai2017")
     else:
         raise ValueError(f"atlas must be one of {AVAILABLE_ATLASES}")