In stereotactic neurosurgery, computed tomography (CT) and magnetic resonance (MR) images are registered in a coordinate system defined with respect to the skull. By intraoperatively tracking the coordinate position of a surgical instrument, various displays can be formed which show the position of the instrument in the MR and/or CT images. However, the accuracy of this display varies because intracranial structures may shift or warp from their position prior to surgery. Ultrasonic imaging systems provide real-time images of the brain, but structures in these images are difficult to interpret because the images are based on ultrasonic echoes. A method has been developed for the real-time registration of these images. With this registration, software continuously updates a corresponding image constructed from the set of MR and/or CT images used for guidance. By developing this second view of the structures in the ultrasound image, the surgeon can easily interpret the ultrasound image, and it becomes possible to determine the extent of the intra-operative structure shift between the two images.