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Magnetic resonance (MR) imaging has recently been proposed for assessing osteoporosis and predicting fracture risks. However, accurate acquisition techniques and image analysis protocols for the determination of the trabecular bone structure are yet to be defined. The aim of this study was to assess the potential of projection reconstruction (PR) MR microscopy in the analysis of the three-dimensional (3-D) architecture of trabecular bone and in the prediction of its biomechanical properties. High-resolution 3-D PR images (41 × 41 × 82 μm3 voxels) of 15 porcine trabecular bone explants were analyzed to determine the trabecular bone volume fraction (Vv), the mean trabecular thickness (Tb.Th), and the mean trabecular separation (Tb.Sp) using the method of directed secants. These parameters were then compared with those derived from 3-D conventional spin-echo microimages. In both cases, segmentation of the high-resolution images into bone and bone marrow was obtained using a spatial adaptive threshold. The contemporary inclusion of Vv, Tb.Th and 1/Tb.Sp in a multiple regression analysis significantly improved the prediction of Young's modulus (YM). The parameters derived from the PR spin-echo images were found to be stronger predictors of YM (R2 = 0.94, p = 0.004) than those derived from conventional spin-echo images (R2 = 0.79, p = 0.051). Our study indicates that projection reconstruction MR microscopy appears to be more accurate than the conventional Fourier transform method in the quantification of trabecular bone structure and in the prediction of its biomechanical properties. The proposed PR approach should be readily adaptable to the in vivo MRI studies of osteoporosis.