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In breast conserving surgery clinicians may benefit from information from preoperative images (e.g. high quality dynamic contrast enhanced magnetic resonant image obtained in the prone position), by registering them to the supine patient on the operating table in the theatre. Due to large deformation involved between prone and supine, either non-rigid intensity-based mage registration methods or biomechanical model based methods alone have limited success. In this paper, we proposed a hybrid finite element method (FEM) based image registration method by combining patient-specific biomechanical models with nonrigid intensity-based image registration methods. FEM-based biomechanical models were used to estimate the major deformation of breasts while non-rigid intensity based image registration methods were used to recover the difference between experimental acquisitions and FE predictions due to the simplifications and approximations of biomechanical models. The proposed method shows a good performance for image registration, demonstrated by the experimental example of prone and supine MR breast image registration.