A surface matching technique has been developed to register multiple imaging scans of the brain in three dimensions, with accuracy on the order of the image pixel sizes. Anatomic information visualized in X-ray CT and magnetic resonance images may be integrated with each other and with functional information from positron emission tomography. Anatomical structures and other volumes of interest may be mapped from one scan to another, and corresponding sections through multiple scans may be directly compared. This capability provides a novel quantitative method to address the fundamental problem of relating structure to function in the brain. Applications include basic and clinical problems in the neurosciences and delivery and assessment of brain tumor therapy.