A system and method for registering pre-operative magnetic resonance (MR) images with intra-operative MR images is disclosed. A pre-operative MR image of an object is received. A set of intra-operative MR images of the object is received. The pre-operative MR image is rigidly registered with the initial intra-operative MR image. The subsequent set of intra-operative images is deformably registered. The pre-operative MR image undergoes both rigid and deformation transformation to match specification of each image with in intra-operative MR image set.