The Automatic Surface Labeling Process; GCA Atlases
This document provides an overview of two related topics:
How the FreeSurfer pipeline automatically labels a subject's regions (producing an annotation file) by comparing the subject's curvature data to an "atlas" ("gcs") file.
The process of creating one's own atlas file, perhaps to define regions different from the ones mapped in the atlases supplied with FreeSurfer.
The Labeling Process
First, the labeling process depends on the subject having already been through the spherical registration process (ie: having a ?h.sphere.reg file), because the atlas data is in the same space as the registration template. This is the case for the recon-all FreeSurfer pipeline script. (The separate topic of sperical registration is described here: SurfaceRegAndTemplates.)
The labeling process itself is diagrammed below.
Program mris_ca_label inputs