When correcting attenuation in a nuclear image (e.g., PET or SPECT), an MR-based attenuation correction (AC) map (16) is generated using MR image data (14) of a subject (60). The subject (60) is then placed in a nuclear imaging device with a radioactive point or line source (18, 18′) from which transmission data is measured as the patient is imaged. In order to resolve ambiguity between air voxels and bone voxels in the MR-based AC map (16), estimated transmission data (24) is generated from the AC map and compared to the measured transmission data (22) from the point or line source. An error is iteratively calculated for the estimated and measured transmission data, and attenuation values of the AC map (16) are refined to minimize the error. The refined AC map (32) is used to correct attenuation in collected nuclear data (41) which is reconstructed into an attenuation corrected image (99) of the patient.