1. A method of correcting susceptibility artefacts in an acquired magnetic resonance image comprising the steps of: performing phase unwrapping for an acquired magnetic resonance (MR) image, including computing a confidence for the phase unwrapping for each voxel of the acquired MR image; generating a field map for the acquired magnetic resonance image from the unwrapped phase; converting the field map to a deformation field; and using the deformation field to initialise a non-rigid image registration of the acquired MR image against a reference image, wherein the deformation field of the non-rigid registration is controlled to be smoother where said confidence is high.