The invention provides for a medical imaging system (100, 300, 400) comprising a memory (110) containing machine executable instructions (120) and a processor (106). Execution of the machine executable instructions cause the processor to: receive (200) a magnetic resonance image (300), receive (202) meta data descriptive of the magnetic resonance image, wherein the metadata comprises reference gray scale value data (124) for two or more tissue types; and segment (204) the magnetic resonance image using an image segmentation algorithm (126) that uses the reference gray scale value data.