Abstract: A particle therapy apparatus configured to scan a charged particle beam over a target according to a pre-defined treatment field which covers a treatment surface in an isocenter plane of the apparatus. The apparatus is capable of scanning the beam over a reachable surface which covers and is larger than the treatment surface. A beam stopper is arranged downstream of the scanning magnets of the apparatus, at a position to prevent the beam from reaching at least a portion of the reachable surface and to allow the beam to reach any portion of the treatment surface. A control system is configured to control the apparatus to direct the beam to the beam stopper and to meanwhile measure a position of the beam, to calculate a difference between a desired position and the measured position of the beam when directed to the beam stopper, and to scan the beam over the target according to the pre-defined treatment field by taking into account the calculated difference.