1. A brain registration system, comprising: a main magnet configured to create a strong, static magnetic field through an imaging volume; magnetic field gradient coils configured to generate magnetic field gradients in the imaging volume; one or more RF coils configured to transmit radio frequency pulses into the imaging volume and receive magnetic resonance echo signals from the imaging volume; a transmitter configured to control the one or more RF coils to transmit magnetic resonance excitation and manipulation pulses into the imaging volume; one more receivers configured to demodulate the magnetic resonance echo signals from the one or more RF coils; a back end system including a memory configured to store brain templates, a user input device, a display device, and one or more processors configured to: reconstruct the demodulated magnetic resonance echo signals from the receiver into a brain image, segment the brain image to annotate brain image data, globally register the brain image with a template image retrieved from the storage memory, identify an articulated structure in the segmented brain image, the articulated structure including a pair of sub-structures connected by a linking joint, rotate the articulated sub-structures relative to each other about the linking joint to improve registration to maximize image similarity of the articulated structure in the brain image and the brain template, and control the display device to display the brain image including the articulated structure.