Query multiple FreeSurfer surface atlases with MultiAtlasMapper

This example mirrors the multi-atlas tutorial but uses three FreeSurfer-based surface parcellations via MNE:

• aparc

• aparc.a2009s

• aparc.a2005s

We batch-map MNI coordinates to region names across these atlases.

1. Imports

from coord2region.fetching import AtlasFetcher
from coord2region.coord2region import MultiAtlasMapper
import mne
from pathlib import Path

2. Define atlases and initialize MultiAtlasMapper Explicitly prefer the MNE backend for FreeSurfer atlases.

af = AtlasFetcher()
# Try to locate a subjects_dir for FreeSurfer (optional but recommended)
subjects_dir = mne.get_config("SUBJECTS_DIR", None)
if subjects_dir is None:
    try:
        subjects_dir = str(Path(mne.datasets.sample.data_path(download=False)) / "subjects")
    except Exception:
        subjects_dir = None
common = {"prefer": "mne", "subject": "fsaverage"}
if subjects_dir is not None:
    common = {**common, "subjects_dir": subjects_dir}

atlases = {
    "aparc": {**common},
    "aparc.a2009s": {**common},
    "aparc.a2005s": {**common},
}
multi = MultiAtlasMapper(data_dir=af.data_dir, atlases=atlases)
print(f"Loaded {len(multi.mappers)} surface atlases.")

3. Batch map MNI coordinates to region names across the atlases

mni_coords = [
    [-42, -22, 10],
    [40, -25, 15],
    [-10, -70, 20],
]
results = multi.batch_mni_to_region_names(mni_coords)
for atlas_name, names in results.items():
    print(f"\nAtlas: {atlas_name}")
    for coord, name in zip(mni_coords, names):
        print(f"  MNI {coord} → {name}")

4. Summary - Initialized multiple FreeSurfer surface atlases - Compared region-name lookups for the same coordinates across parcellations