A method of operating a radiotherapy system mounted on a gantry surrounding a magnetic resonance imaging system is provided, the radiotherapy system comprising a radiotherapy beam generator, and a radiotherapy imaging system, wherein the gantry is arranged to rotate the radiotherapy beam generator around the magnetic resonance imaging system. The method comprises obtaining a reference image, the reference image including a predetermined feature of the magnetic resonance imaging system located near the radiotherapy imaging system; rotating the gantry relative the magnetic resonance imaging system; obtaining a second image, the second image including the predetermined feature of the magnetic resonance imaging system located near the radiotherapy imaging system; and determining changes in the relative positions of the radiotherapy beam generator, the radiotherapy imaging system, and the magnetic resonance imaging system based on differences in the position of the predetermined feature in the reference image and in the further image.