We present a method for registration of macroscopic optical images with MR images of the same patient. This forms a key part of a series of procedures to allow post mortem findings to be accurately registered with MR images, and more generally provides a method for 3D mapping of the distribution of pathological changes throughout the brain. The first stage of the method involves a 3D reconstruction of 2D brain slices and was presented in a previous paper [2]. In the current paper, we focus on the registration of the reconstructed volume with corresponding MR images.