Deformable image registration (DIR) is one of the major problems in medical image processing, such as dose calculation [18], treatment planning [33] and scatter removal of cone beam CT (CBCT) [22]. It is of prime importance to establish a pixel-to-pixel correspondence between two images in many clinical scenarios. For instance, registration of a CT image to MRI of a patient taken at different time can provide complementary diagnostic information. For applications as such, since the deformation of the patient anatomy cannot be represented by a rigid transform, DIR is almost the sole means to establish this mapping. DIR can be generally categorized into intra-modality and inter-modality, or multi-modality. While intra-modality DIR can be easily handled by conventional intensity-based methods [11, 30], intermodality DIR problems are still far from being satisfactory. Yet, since different imaging modalities usually provide their unique angles to reveal patient anatomy and delineate microscopic disease, intermodality registration plays a key role to combine the information from multiple modalities to facilitate diagnostics and treatment of a certain disease.