Quantitative interpretation of functional images (PET or SPECT) is hampered by poor spatial resolution, low counting statistics and, for many tracers, low contrast between different brain structures of interest. Further, normal tracer distributions can be severely distorted by such gross pathologies as stroke, tumor and dementia. Hence, the complementary anatomical information provided by CT or MRI is essential for accurate and reproducible regional analysis of functional data. We have developed methods for the three-dimensional integration and simultaneous display of image volumes from MRI and PET. PET data was collected from an older Therascan 3-slice scanner with 12 mm resolution and a 15-slice Scanditronix PC-2048 system having 5-6 mm resolution in each dimension. MRI data was obtained from a Philips 1.5 Tesla Gyroscan scanner. The image volumes were loaded into a PIXAR 3-D image computer for simultaneous display. A general algorithm for finding the optimal transformation between two ensembles of equivalent points was implemented and investigated through simulation studies. Using a locally-developed 3-D image/graphics analysis package, equivalent points in the two image volumes were identified, either manually or via an adjustable computerized volume-of-interest (VOI) atlas. The MRI data were then re-sampled along planes parallel to the PET planes and the two volumes overlaid using opacity-weighted composition. Arbitrary oblique planes through the two volumes were obtained in interactive sessions.