A method for multimodal image registration includes providing a pair of images acquired from differing imaging modalities, defining an intensity correction function that corrects the intensities of a first image in terms of the intensities of the second image, defining a registration transformation function that registers the second image with the first image, wherein said intensity correction function and transformation function are functions of a plurality of parameters, obtaining corrections to the plurality of parameters by minimizing an energy functional of a square difference of the intensity corrected first image and the registration transformed second image, and updating the intensity correction function and the registration transformation function based on the corrected plurality of parameters.