atlas

classes.atlas

Attributes

Name	Description
aseg_gm_regions
atlas_data
available_atlases

Classes

Name	Description
Atlas	BrainAtlas with lazy, computed properties for data files and derived attributes.

Atlas

classes.atlas.Atlas(atlas=None, **kwargs)

BrainAtlas with lazy, computed properties for data files and derived attributes.

Usage mirrors other runtime wrappers (Dynamics, SimulationExperiment): - Construct from a BrainAtlas instance, a string name, or nothing (defaults to ‘wholebrain’). - Access metadata to get a self-reference as a LinkML object. - Access properties: volume, volume_file, metadata_file, region_labels, centers.

SANDS entities are stored in self.terminology.entities — a schema-native dict[ParcellationEntityName, ParcellationEntity] produced by the LinkML loader (the entities slot uses inlined: true in the SANDS schema).

Attributes

Name	Description
centers	Region center coordinates as (N, 3) array.
region_labels	Region labels sorted by SANDS lookupLabel.

Methods

Name	Description
create_terminology	Build terminology entities from the atlas volume if not already populated.

create_terminology

classes.atlas.Atlas.create_terminology()

Build terminology entities from the atlas volume if not already populated.

Functions

Name	Description
create_atlas_metadata
rank_atlas
tqdm

create_atlas_metadata

classes.atlas.create_atlas_metadata(fname_atlas, labels='freesurfer')

rank_atlas

classes.atlas.rank_atlas(
    fname_atlas,
    labels='freesurfer',
    desc='ranked',
    gm_only=True,
)

tqdm

classes.atlas.tqdm(x, **kwargs)