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Failure of accurate registration of the follow\u2010up to the baseline images introduces errors due to the inherent anisotropy in the trabecular network and anisotropic voxel size. In this work it is shown that these limitations can be overcome by incorporating on\u2010line prospective registration into the data acquisition protocol. The technique is based on a short 3D localizer scan of 1 mm isotropic resolution prior to acquiring the high\u2010resolution images. During the follow\u2010up exam, localizer images are registered on\u2010site with an algorithm relying on a fast Fourier transform for maximizing the correlation between baseline and follow\u2010up localizers. Transformation parameters obtained in this manner are then fed into the scanner software so that the imaging slab for the high\u2010resolution follow\u2010up images is automatically positioned consistent with that of the baseline scan. Based on phantom and human subject studies it is shown that prospective registration yields very close matching between baseline and follow\u2010up imaging volumes. 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