A method has been developed to create corresponding brain slices from morphological [CT, magnetic resonance (MR)] and functional [positron emission tomography (PET), single photon emission computed tomography] tomographic studies in individual patients. It does not require special headholders or definition of specific landmarks and is fully retrospective. Three-dimensional image registration in corresponding orientation is achieved by linear interpolation of original slices and a variety of interactively controlled video display options. These include simultaneous display of multiple slices and brain cuts in all three dimensions for comparison of positioning. Brain contours in one imaging modality may be enhanced by appropriate filtering and superimposed onto reference images of another modality. Matching accuracy depends on image resolution; misalignment of 4 mm was detected unambiguously in sample studies (fluoro-2-deoxy-D-glucose PET matched with MR). The technique is equally well applicable to normals and to patients with structural brain lesions. Additional options for shaded surface display enhance the power to identify neuroanatomical structures in functional image analysis. As demonstrated in the example of MR-guided PET, this modeling procedure can be successfully used for identification of brain structures on functional images, even in patients with pathologically altered brain morphology.