In a method for operating a medical imaging apparatus having subsystems, a control protocol assigned to a scan sequence to be performed is provided to a control computer that determines sequence control data for the control protocol, which define different functional subsequences of the scan sequence. Different effective volumes are assigned to each functional subsequence, and current ambient conditions of the apparatus are determined for the sequence control data and associated effective volumes, for a series of states of physiological processes that occur during the scan sequence. Control signals for the scan sequence are determined from the sequence control data, the effective volumes and the current ambient conditions per observed state, that optimize the functional subsequences of the scan sequence locally. During the scan, at least one current state of the observed physiological processes is determined and the control signals used for the ongoing scan are determined from the stored control signals, dependent on the at least one current state.