Adaptation of image data sets to an updated atlas-based reference system

The invention relates to a computer-implemented medical data processing method for determining a mapping of medical image content into a reference system, the method comprising executing, on a processor of a computer, steps of: a) acquiring, at the processor, medical image data describing a digital medical image of an anatomical structure of a patient's body; b) acquiring, at the processor, image attribute data describing attribute information associated with the medical image data, the attribute information including an indication of an initial reference system in which spatial relationships of the digital medical image are defined; c) acquiring, at the processor, reference system transformation data describing a spatial relationship (REG) between the initial reference system and a second reference system which is different from the initial reference system; d) determining, by the processor and based on the medical image data and the reference system transformation data, transformed image data describing a representation of the digital medical image in the second reference system.