1. A method for registering a source image with a target image, wherein the images are deformable, comprising: measuring dissimilarity between the source image and the target image; minimizing the dissimilarity using a discrete energy function; applying, at multiple scales, multi-scale Markov random field registration to the source and target images to determine a deformation vector field; and warping the target image according to the deformation field vector to obtain a warped target mage registered to the source image, wherein the steps are performed in a processor.