A method and system for magnetic resonance imaging (MRI) based motion correction in position emission tomography (PET) images is disclosed. A static 3D magnetic resonance (MR) image of a patient is received. PET image data of the patient and a series of 2D MR images of the patient acquired simultaneous to the acquisition of the PET image data are received. A 3D+t motion field is estimated by registering the series of 2D MR images acquired at the plurality of time points to the static 3D MR image. A motion corrected PET image is generated based on the estimated 3D+t motion field using motion corrected PET reconstruction.
