1. A treatment planning apparatus comprising a means for receiving a three dimensional representation of a patient, a means for displaying at least a part of the representation, a means for user-designation of sub-regions of the representation, and a computing means adapted to segment the representation into a region within an anatomical structure and a region outside the anatomical structure on the basis of the locations of the sub-regions, the degree of similarity of voxels to neighbouring voxels in the representation, and a dataset representing an a priori assumption of the correct segmentation.