The thorax structure movements (breathing, heart motion and patient motion) during the positron emission tomography (PET) scanning cause deformations and blurring to PET scans. These artifacts are important reasons, for the misregistration of PET volumes. In this paper, a breathing simulated PET phantom was constructed by deforming simulated (static) PET volume according to breathing model. The constructed volume was used as a ground truth in the assessment of a nonrigid registration method for cardiac MR and PET volumes. Results showed that the assessed nonrigid registration method was more accurate than a rigid registration method which was used as a reference.