1. A computer-implemented method of processing medical image data, comprising: accessing a computed tomography image of a brain; accessing an atlas having anatomical information referenced to a coordinate system, wherein the atlas comprises brain images taken with a magnetic resonance imaging system; aligning the computed tomography image with the atlas, wherein aligning the computed tomography image with the atlas comprises aligning using a rigid or affine transform followed by a piece-wise affine correction constrained by the coordinate system; transforming the computed tomography image to the coordinate system of the atlas; and labeling the computed tomography image with the anatomical information from the atlas.