1. A system that facilitates resolving ambiguity in a magnetic resonance (MR) image or attenuation map, including: an MR reconstruction processor that generates an MR image from raw MR data acquired during a scan of a subject by an MR scanner; a functional image reconstruction processor that generates a functional image from functional image data acquired during a scan of a subject by a functional image scanner; and a processor programmed to: segment the MR image to generate a segmented MR image having a region of air/bone ambiguity in which ambiguity between air voxels and bone voxels is unresolved; segment the functional image to generate a segmented functional image having bone regions; compare bone regions in the segmented functional image to the bone/air ambiguity region in the segmented MR image to resolve ambiguity between voxels in the bone/air region in the segmented MR image, which correspond to bone and air; assign radiation attenuation values consistent with bone to identified hone voxels, and consistent with air to identified air voxels, in the segmented MR image; and generate an MR attenuation map using the assigned radiation attenuation values.