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As bone mineral density has been demonstrated to be insufficient to elaborate a correct diagnosis of bone diseases such as osteoporosis, a new software tool called EsTra has been developed in order to estimate the most significant structural parameters of trabecular bone microarchitecture. In EsTra, different techniques as automated segmentation, snakes, filtering, skeletonization, voxel classification and three-dimensional reconstruction are applied to Magnetic Resonance images of distal radius and ulna. A microarchitectural study is also carried out from three different viewpoints involving morphological, topological and fractal analysis. Results can be exported to a database to help the research of the disease and a clinical report is elaborated containing the most significant parameters obtained from the analysis.