When generating a magnetic resonance (MR) attenuation map (39), an MR image is segmented to identify a patient's body outline, soft tissue structures, and ambiguous structures comprising bone and/or air. To distinguish between bone and air in the ambiguous structures, a nuclear emission image (e.g., PET) of the same patient or region of interest is segmented. The segmented functional image data is correlated to the segmented MR image data to distinguish between bone and air in the ambiguous structures. Appropriate radiation attenuation values are assigned respectively to identify air voxels and bone voxels in the segmented MR image, and an MR attenuation map is generated from the enhanced segmented MR image, in which ambiguity between air and bone has been resolved. The MR attenuation map is used to generate an attenuation-corrected nuclear image, which is displayed to a user.