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PURPOSE To develop free-running multi-echo GRE for cardiac- and respiratory-motion-resolved whole-heart fat fraction quantification. METHODS Multi-echo readouts optimized for water-fat separation and quantification were integrated within a non-ECG-triggered free-breathing 3D radial GRE acquisition. Pilot Tone navigation was used to extract cardiac and respiratory motion states. Following a XD-GRASP based image reconstruction of the separate echoes, fat fraction, water fraction, R2star and B0 maps, as well as fat and water images, were generated with a maximum likelihood fitting algorithm using graph cuts. The acquisition, reconstruction and post-processing framework was tested in 10 healthy volunteers at 1.5T and compared to a free-breathing ECG-triggered 5-echo acquisition. RESULTS The acquisition was successfully validated in vivo, with motion compensation achieved over all collected echoes, in both respiratory and cardiac dimensions. Pilot Tone navigation provided respiratory and cardiac signals in good agreement (r=0.954 and r=0.783, respectively) with self-gating signal extraction based on the MR data of the first echo. The framework enabled pericardial fat imaging and quantification across the cardiac cycle, revealing a decrease in apparent FF at systole across volunteers. 3D motion-resolved fat fraction maps showed good correlation with reference ECG-triggered measurements, as well as significant difference in measurements performed with NTE = 4 and NTE = 8 echoes (P < 0.0001 in chest fat and P < 0.01 in pericardial fat). CONCLUSION Volunteer experiments at 1.5T demonstrated the feasibility of a whole-heart free-running fat-fraction mapping technique for cardiac MRI in a 6 min scan time, with a resolution of 2mm3 isotropic., Comment: 38 pages, 9 figures, accepted in Magn Reson Med