This disclosure presents an improved method for registering anatomical medical images and functional medical images. The example deals with the registration of x-ray computer tomography images with positron emission tomography images. The process is characterized by clinically useful registration with minimal computer calculations and minimal delay for computation. A nonrigid B-Spline free form deformation is used in both a preliminary coarse registration and the finished fine registration. Additional steps are used to insure accurate and complete registrations.