An x-ray apparatus has a flat panel x-ray detector, the operation of which is susceptible to interference by strong magnetic fields. In order to allow the x-ray system to be operated concurrently with a magnetic system, such as a magnetic tracking system or a magnetic localization system, that emits a magnetic field of sufficient field strength to interfere with the operation of the flat panel x-ray detector, a control unit is provided that operates both the flat panel x-ray detector and the magnetic system. The control unit synchronizes operation of the magnetic system with the operation of the flat panel x-ray detector so that the magnetic system emits the magnetic field only at times that do not interfere with the operation of the flat panel x-ray detector.