1. A medical image processing system, comprising a computer which is configured to execute a computer-implemented medical image processing method of matching a medical image of an anatomical structure of a patient's body with an atlas-based representation of the anatomical structure, the medical image processing method comprising executing, on at least one processor of a computer, steps of: acquiring, by the at least one processor, patient image data describing a medical image representation of the anatomical structure in the medical image; determining, by the at least one processor and based on the patient image data, patient substructure data describing a plurality of patient substructure representations each describing a different patient substructure of the anatomical structure; acquiring, by the at least one processor, general substructure data describing a general substructure representation of each of a plurality of general substructures for each of the patient substructures; determining, by the at least one processor and for each of the patient substructures and based on the patient substructure data and the general substructure data, substructure matching data describing a matching general substructure representation which, without being deformed, matches the respective patient substructure representation; outputting, by the at least one processor and based on the general substructure data and the substructure matching data, anatomical structure atlas data describing an atlas representation of the anatomical structure; determining, by the at least one processor and based on the patient image data and the anatomical structure atlas data, matching transformation data describing an atlas-patient matching transformation between the medical image representation of the anatomical structure and the atlas representation of the anatomical structure.