abagen.check_atlas¶
- abagen.check_atlas(atlas, atlas_info=None, geometry=None, space=None, donor=None, data_dir=None)[source]¶
Checks that atlas is a valid atlas
- Parameters
atlas (niimg-like object or (2,) tuple-of-GIFTI) – Parcellation image or surface, where voxels / vertices belonging to a given parcel are identified with a unique integer ID
atlas_info ({os.PathLike, pandas.DataFrame, None}, optional) – Filepath or dataframe containing information about atlas. Must have at least columns [‘id’, ‘hemisphere’, ‘structure’] containing information mapping atlas IDs to hemisphere (i.e., “L”, “R”, “B”) and broad structural class (i.e.., “cortex”, “subcortex/brainstem”, “cerebellum”, “white matter”, or “other”). Default: None
geometry ((2,) tuple-of-GIFTI, optional) – Surfaces files defining geometry of atlas, if atlas is a tuple of GIFTI images. Default: None
space ({'fsaverage', 'fsnative', 'fslr'}, optional) – If geometry is supplied, what space files are in. Default: None
donor (str, optional) – If specified, indicates which donor the specified atlas belongs to. Only relevant when atlas is surface-based, to ensure the correct geometry files are fetched. Default: None (i.e., group-level atlas)
data_dir (str, optional) – Directory where donor-specific FreeSurfer data should be downloaded and unpacked. Only used if provided donor is not None. Default: $HOME/ abagen-data
- Returns
atlas – AtlasTree object with information about atlas and functionality for labelling coordinates
- Return type