1. A system for generating registered nuclear and MR diagnostic images of a subject, the system comprising: a nuclear imaging device which generates emission diagnostic images, the nuclear imaging device including a radiation source for use in generating the transmission intermediate images, the transmission image being inherently registered with the emission diagnostic image; an MR imaging device which generates magnetic resonance images including magnetic resonance diagnostic images and MR intermediate images, the MR intermediate images being proton density images different from the magnetic resonance diagnostic images, the proton density image being generated by a scan sequence that is interleaved into a scan sequence for generating the MR diagnostic image; one or more processors programmed to: generate a transform which aligns common anatomical structures in at least one of the nuclear intermediate images generated by the nuclear imaging device and the magnetic resonance images generated by the MR imaging device, and applies the transform to bring the emission and magnetic resonance diagnostic images into registration; and wherein the transform is generated based on the nuclear intermediate images and the MR intermediate images.