subcortical_mask

petpal.preproc.segmentation_tools.subcortical_mask(input_seg_path: str, output_seg_path: str = None, subcortical_regions: list = None)

Gets a mask for subcortical regions from a FreeSurfer label image.

Parameters:

• input_seg_path (str) – Path to segmentation label image.

• output_seg_path (str) – Path to which subcortical mask is saved.

• regions (subcortical) – Regions to include in the subcortical mask. Uses a built in list of subcortical mappings unless overridden by the user.

Returns:

subcortical_img (ants.ANTsImage) – Subcortical mask image.

Important

• Subcortical mappings are assumed to correspond to a subset of FreeSurfer subcortical

  regions

• Default regions: whole cerebellum, thalamus, caudate, putamen, pallidum, brainstem.