1. A method for registering a pre-operative image of a patient to an intra-operative image of the patient, comprising: generating an initially registered pre-operative image by estimating deformations of one or more segmented anatomical structures in the pre-operative image using biomechanical gas insufflation model constrained registration with the intra-operative image; and refining the initially registered pre-operative image using diffeomorphic non-rigid refinement.