Abstract: A positron emission tomography-magnetic resonance (PET-MR) system is provided. The PET-MR system includes an MR subsystem, a PET subsystem, and a protocol adjustment system. The protocol adjustment system includes a protocol adjustment computing device having at least one processor programmed to receive a protocol. The protocol includes a scanning task list including a PET scanning task of a bed and MR scanning tasks of the bed and to be performed simultaneously with the PET scanning task. The protocol also includes a combination list indicating MR data acquired by an MR scanning task of one bed are to be combined with MR data acquired by the same MR scanning task of another bed. The at least one processor is further programmed to adjust the protocol based on the combination list by processing the one or more MR scanning tasks based on the combination list.