The invention provides for a medical instrument (200, 300, 400, 500, 600, 700) comprising a magnetic resonance imaging system (204) operable for acquiring magnetic resonance data (266) from a subject (236) within an imaging zone (232) and an external beam radiotherapy system (202) operable for irradiating a target zone (238) within the imaging zone. The medical instrument further has a radiation beam generation system (208, 302, 302′, 302″) operable for generating a radiation beam (242, 304, 304′, 304″) and a radiation beam detection system (243, 502, 502′) operable for acquiring radiation beam detection data (270) descriptive of the radiation beam. Instructions cause a processor (248) controlling the instrument to receive (100) planning data (260) descriptive of a spatially dependent radiation dose and generate (102) external beam radiotherapy control commands (264) using the radiation dose. The instructions causes the processor to repeatedly: control (106) the external beam radiotherapy system to irradiate the target zone using the external beam radiotherapy system control commands； generate (108) the radiation beams using the radiation beam generation system； measure (110) the radiation beam detection data using the radiation beam detection system； acquire (112) the magnetic resonance imaging data using the magnetic resonance imaging system, generate (114) a magnetic resonance image (268) using the magnetic resonance image data, determine (116) a registration (274) of the magnetic resonance image to the radiation beam detection data； calculate (118) a mapping (276) using the registration； and modify the external beam radiotherapy system control commands using the mapping.
