Complementary morphological information is a prerequisite for the detailed analysis of cerebral SPET studies. We therefore developed a technique which allows the alignment of SPET and magnetic resonance scans by imaging identical slices using external landmarks on an individually fitted mask and subsequent two-dimensional image processing for in-plane matching. Regional analysis of tracer activities can be performed directly on the superimposed SPET and MR outline images or by tracing a region of interest on the original MR scan with a parallel display on the matched SPET image, and vice versa. Tests assessing correct in-plane alignment using MRI, inter- and intra-variability of the matching procedure, and its comparability with an objectively determined best-matching position, confirmed the feasibility, accuracy and usefulness of this procedure.