One method used to correct geometric and intensity distortions in echo planar images is to register them to undistorted images via nonrigid deformations. However, some areas in the echo planar images are more distorted than others, thus suggesting the use of deformations whose characteristics are adapted spatially. In this article, we incorporate into our previously developed registration algorithm a spatially varying scale mechanism, which adapts the local scale properties of the transformation by means of a scale map. To compute the scale map, a technique is proposed that relies on an estimate of the expected deformation field. This estimate is generated using knowledge of the physical processes that induce distortions in echo planar images. We evaluate the method of spatially varying scale on both simulated and real data. We find that, in comparison with our earlier method using fixed scale, our new method finds deformation fields that are smoother and finds them faster without sacrificing accuracy.