subcortical_mask
==================================================

.. py:function:: 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.

   :param input_seg_path: Path to segmentation label image.
   :type input_seg_path: str
   :param output_seg_path: Path to which subcortical mask is saved.
   :type output_seg_path: str
   :param subcortical regions: Regions to include in the subcortical mask. Uses a built in
                               list of subcortical mappings unless overridden by the user.
   :type subcortical regions: list

   :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.