1. A method for compensating motion artifacts in positron emission tomography (“PET”) imaging based on medical images acquired with a medical imaging system, the method comprising: a) acquiring PET data from a subject with a PET system during which motion of at least a portion of the subject is occurring; b) providing medical images acquired from the subject using a medical imaging system, the medical images including regions depicting motion; c) estimating, from the medical images, motion information indicative of the motion of the at least a portion of the subject that occurred in step a); and d) reconstructing a motion-corrected PET image using the PET data and a reconstruction algorithm that incorporates the estimated motion information into a system matrix.