In a magnetic resonance apparatus, a check is performed as to whether coordinate-transformed first values of system parameters of a scan protocol for a magnetic resonance scan sequence each comply with a corresponding limit value. The check is used as the basis for the adaptation of first values of scan parameters of the scan protocol in order to obtain second values of the scan parameters. The second values of the scan parameters are used as the basis for the adaptation of the coordinate-transformed first values of the system parameters in order to obtain second values of the system parameters.