Accurate localization and uptake quantification of lesions in the chest and abdomen using PET imaging is challenging due to the respiratory motion during the exam. The advent of hybrid PET/MR systems offers new ways to compensate for respiratory motion without exposing the patient to additional radiation. The use of self-gated reconstructions of a 3D radial stack-of-stars GRE acquisition is proposed to derive a high-resolution MRI motion model. The self-gating signal is used to perform respiratory binning of the simultaneously acquired PET raw data. Matching mu-maps are generated for every bin, and post-reconstruction registration is performed in order to obtain a motion-compensated PET volume from the individual gates. The proposed method is demonstrated in-vivo for three clinical patients. Motion-corrected reconstructions are compared against ungated and gated PET reconstructions. In all cases, motion-induced blurring of lesions in the liver and lung was substantially reduced, without compromising SNR as it is the case for gated reconstructions.