This paper presents a method for the coregistration and partitioning (i.e., tissue segmentation) of brain images that have been acquired in different modalities. The basic idea is that instead of matching two images directly, one performs intermediate within-modality registrations to two template images that are already in register. One can use a least-squares minimization to determine the affine transformations that map between the templates and the images. By incorporating suitable constraints, a rigid body transformation which directly maps between the images can be extracted from these more general affine transformations. A further refinement capitalizes on the implicit normalization of both images into a standard space. This facilitates segmentation or partitioning of both original images into homologous tissue classifications. Once partitioned, the partitions can be jointly matched, further increasing the accuracy of the coregistration. In short, these techniques reduce the between-modality problem to a series of simpler within-modality problems. These methods are relatively robust, address a number of problems in image transformations, and require no manual intervention.