The goal of this study was to compare two approaches for MR-based PET patient attenuation correction (AC) in whole-body FDG-PET imaging using a tri-modality PET/CT and MR setup. Sixteen clinical whole-body FDG patients were included in this study. Mean standard uptake values (SUVs) were measured for liver and lung volumes-of-interest for comparison. Maximum SUVs were measured in 18 FDG-avid features in 10 of the patients. The AC methods compared to gold-standard CT-based AC were segmentation of the CT (air, lung, fat, water), MR image segmentation with four tissue classes (air, lung, fat, water), and segmentation with air, lung and a continuous fat/water method. Results show that magnitude differences of the uptake values induced by CT-based image segmentation were similar but lower on average than those found using MR-derived AC methods. The average liver SUV difference as compared to using CTAC was 1.3%, 10.4%, and 5.7% for 4-class segmented CT, 4-class MRAC, and continuous fat/water MRAC methods, respectively. The average FDG-avid feature SUVmax difference was -0.5%, 1.7%, and -1.6% for 4-class segmented CT, 4-class MRAC, and continuous fat/water MRAC methods, respectively. The results demonstrated that both 4-class and continuous fat/water AC methods provided adequate quantitation in the body, and that the continuous fat/water method was within 5.7% on average for SUVmean in liver and 1.6% on average for SUVmax for FDG-avid features.