The invention provides for a medical instrument (100, 500) comprising a magnetic resonance imaging system (102) for acquiring magnetic resonance data (142) from a subject (118) within an imaging zone (108). The magnetic resonance imaging system comprises: a main magnet (104) for generating a B0 magnetic field within the imaging zone; a memory (134, 136) containing machine executable instructions (160, 162, 164, 166) and pulse sequence commands (140); a processor (130) for controlling the medical instrument. Execution of the machine executable instructions causes the processor to: acquire (200) the magnetic resonance data by controlling the magnetic resonance imaging system with the pulse sequence commands; receive (202) a subject magnetic susceptibility map (144) of the subject; calculate (204) a B0 inhomogeneity map (146) from the magnetic resonance data; calculate (206) a subject B0 magnetic field perturbation (148) from the subject magnetic susceptibility map; calculate (208) a residual B0 magnetic field perturbation (150) by subtracting the subject B0 magnetic field perturbation from the B0 inhomogeneity map; and calculate (210) a bone map (152) from the residual B0 magnetic field perturbation.