Abstract: A system for generating registered diagnostic images (58, 62), such as nuclear and magnetic resonance (MR) images, of a subject includes a nuclear imaging device (10) for generating emission diagnostic images (58) and optionally also intermediate transmission or emission images (56). A second imaging device (12), such as an MR imaging device generates magnetic resonance diagnostic images (62) and optionally also intermediate images which are more readily registered with images from the nuclear imaging device than the diagnostic MR images. Processing for the images includes a preprocessing portion (64) for generating a transform for aligning common anatomical structures in images (56, 58, 60, 62) generated by the nuclear imaging device and the MR imaging device and a diagnostic image registration portion for applying the transform to bring the emission and magnetic resonance diagnostic images into registration (58, 62).