The present invention is directed to a method and apparatus for fusing or combining functional image data and anatomical image data. The invention, which may be carried out through user interaction or automatically, enables composite and clinically valuable images to be generated that display functional and anatomical data acquired with different imaging systems. By identifying fiducial markers on a functional data image and correlating the fiducial markers with anatomical markers or indicia on the anatomical data image, the respective images may be aligned with one another before a composite image is generated.