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Objectives: The objective of this study is to demonstrate a new method for analyzing trabecular bone volume fraction and degree of anisotropy in three dimensions., Methods: We use a combination of automatic mesh registration, point-cloud correspondence registration, and P-value corrected univariate statistical tests to compare bone volume fraction and degree of anisotropy on a point by point basis across the entire calcaneus of two human groups with different subsistence strategies., Results: We found that the patterns of high and low bone volume fraction and degree of anisotropy distribution between the Black Earth (hunter-gatherers) and Norris Farms (mixed-strategy agriculturalists) are very similar, but differ in magnitude. The hunter-gatherers exhibit higher levels of bone volume fraction and less anisotropic trabecular bone organization. Additionally, patterns of bone volume fraction and degree of anisotropy in the calcaneus correspond well with biomechanical expectations of relative forces experienced during walking and running., Conclusions: We conclude that comparing site-specific, localized differences in trabecular bone variables such as bone volume fraction and degree of anisotropy in three-dimensions is a powerful analytical tool. This method makes it possible to determine where similarities and differences between groups are located within the whole skeletal element of interest. The visualization of multiple variables also provides a way for researchers to see how the trabecular bone variables interact within the morphology, and allows for a more nuanced understanding of how they relate to one another and the broader mechanical environment., (© 2020 Wiley Periodicals LLC.)