A method and system for automated magnetic resonance (MR) scan prescription is disclosed. A 3D MR scout image is obtained by an initial MR scan. The location of an optic nerve in the scout image is determined by registering a template image to the scout image using a hierarchical series of rigid registrations. The hierarchical series of rigid registrations utilizes a coarse to fine scheme to register regions in the template image to the scout image, starting with the whole template image and finishing with the optic nerve. A diagnostic MR scan is then aligned based on the location of the optic nerve in the scout image, and the diagnostic scan is performed resulting in a high quality diagnostic 3D MR image.