1. Method for registering a three dimensional (3D) coordinate system with a Medical Positioning System (MPS) coordinate system, the method comprising: acquiring MPS points within an organ within a volume of interest of the body of a patient, the MPS points being associated with the MPS coordinate system; estimating a volumetric model of the organ according to the acquired MPS points; and registering the 3D coordinate system with the MPS coordinate system by matching an extracted 3D image model with the volumetric model, the extracted 3D image model being extracted from a pre-acquired 3D image of the volume of interest, the pre-acquired 3D image and the 3D image model being associated with the 3D coordinate system.