1. A brain registration system, comprising: an annotation module configured to annotate brain image data; a global registration module configured to register the brain image data with template image data using global brain registration; an articulation module configured to articulate articulated sub-structures of a brain structure in the registered brain image to improve registration using articulated sub-structure registration; and a local registration module configured to register the brain structure of the brain image data a corresponding brain structure of the template image data using a local brain sub-structure registration.