Coregistration of functional PET and T1-weighted MR images is a necessary step for combining functional information from PET images with anatomical information in MR images. Several coregistration algorithms have been published and are used in functional brain imaging studies. In this paper, we present a comparison and cross validation of the two most widely used coregistration routines (Friston et al., 1995, Hum. Brain Map. 2: 165-189; Woods et al., 1993, J. Comput. Assisted Tomogr 17: 536-546). Several transformations were applied to high-resolution anatomical MR images to generate simulated PET images so that the exact (rigid body) transformations between each MR, image and its associated simulated PET images were known. The estimation error of a coregistration in relation to the known transformation allows a comparison of the performance of different coregistration routines, Under the assumption that the simulated PET images embody the salient features of real PET images with respect to coregistration, this study shows that the routines examined reliably solve the MRI to PET coregistration problem. (C) 1997 Academic Press.