A method (100) and an apparatus (200) are disclosed for registering an input image and an atlas. The atlas is warped (130) using non-rigid registration. In particular, boundary displacements of structures in the atlas are calculated (132) which register those structures with equivalent structures in the input image. The boundaries of structures in the atlas are then warped (133) according to their respective boundary displacements using topology preserving propagation of boundary points of the structures.