A magnetic resonance imaging system has a superconducting magnet housed within a cryostat, a cryogenic refrigerator that cools within the cryostat, a helium compressor that supplies compressed helium to the cryogenic refrigerator and to receive a return flow of compressed helium from the refrigerator, and a magnet supervisory system controlling operation of the magnet resonance imaging system. An apparatus is provided for controlling the speed and/or timing of operation of the helium compressor in accordance with predefined algorithms in response to system state data.