Exemplary embodiments of the present disclosure are directed to scheduling positron emission tomography (PET) scans for a combined PET-MRI scanner based on an acquisition of MR scout images of a subject. An anatomy and orientation of the subject can be determined based on the MR scout images and the schedule for acquiring PET scans of the subject can be determined from the anatomy of the subject. The schedule generated using exemplary embodiments of the present disclosure can specify a sequence of bed positions, scan durations at each bed position, and whether respiratory gating will be used at one or more of the bed positions.