1. A method for registering pre-operative magnetic resonance (MR) images with intra-operative MR images comprising the steps of: receiving a pre-operative MR image of an object; obtaining an intra-operative MR image of the object; rigidly registering the pre-operative MR image with the intra-operative MR image; and using deformable registration techniques to align subsequent intra-operative MR images and eventually warp the pre-operative MR image using the rigid transformation and the incremental deformation field to match to the most recent state of anatomy as presented by the most recent intra-operative MR image.