Automatic processing of 3D ultrasound (US) is of great interest for the development of innovative and low-cost computer-assisted surgery tools. In this paper, we present a new image-based technique to rigidly register intra-operative 3D US with pre-operative Magnetic Resonance (MR) data. Automatic registration is achieved by maximization of a similarity measure that generalizes the correlation ratio (CR). This novel similarity measure has been designed to better take into account the nature of US images. A preliminary cross-validation study has been carried out using a number of phantom and clinical data. This indicates that the worst registration errors are of the order of the MR image resolution.