Current MRI methods to estimate body tissue compartment volumes rely on manual segmentation, which is laborious, expensive, not widely available outside specialized centers, and not standardized. To address these concerns, a novel, semi-automated image analysis method has been developed. Image acquisition takes about six minutes, and uses widely available MRI pulse sequences. We found that this method permits comprehensive body compartment analysis and provides high repeatability and accuracy. Current and future clinical and drug development studies may benefit from this methodology, as may clinical settings where monitoring change in these measures is desired.