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Respiratory motion blurs positron emission tomography (PET) images in thorax and abdominal regions, and can cause attenuation-related errors in quantitative parameters. In addition, this motion can cause localization error and disappearance of tumor(s) near the diaphragm. Respiratory gated PET imaging, or 4D PET imaging, is an attractive solution. For 4D PET, a surrogate measurement of the patient's breathing is made during the scan, and based on this measurement the list-mode PET data are sorted and reconstructed into multiple images. In several studies, it has been reported that 4D PET imaging recovers tumor volume more accurately than 3D PET imaging, and yields more accurate standard uptake values. In spite of its promise, 4D PET images suffer from statistical noise because only a fraction of the acquired data can be used in each image. Moreover, they also suffer from inconsistent attenuation correction due to mismatches between PET and CT images. In this paper, we propose a novel framework for phased attenuation correction and respiratory motion compensation for a 3D PET image by using a 3D CT image and multiple respiratory-phase 3D MR images. For phased attenuation correction, we generate and utilize 4D CT image obtained via non-rigid registrations among a 3D CT image and multiple respiratory-phase 3D MR images. A 3D PET image at a selected respiratory phase is then obtained by adding attenuation corrected multiple 3D PET images through non-rigid transformation. Experimental result for a clinical dataset shows that the proposed algorithm can provide much clearer organ boundary with improved quality than the conventional method in a 3D PET image.