Chemical shift encoding-based water-fat MRI derived proton density fat fraction (PDFF) of the thigh muscles bears potential as a surrogate marker in subjects with osteoarthritis, sarcopenia, and neuromuscular disorders. Muscle PDFF has shown to correlate with isometric strength at the thigh and spine. However, MR-based muscle fat quantification requires time-consuming segmentation of multiple muscle compartments. Therefore, we investigated if segmentation of single compartment muscles and of different levels of the thigh influences the relation of PDFF to isometric strength. The present study demonstrated that PDFF measurements can be limited to an entire muscle compartment, independent of sampling level.