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We argue that registration should be thought of as a means to an end, and not as a goal by itself. In particular, we consider the problem of predicting the locations of hidden labels of a test image using observable features, given a training set with both the hidden labels and observable features. For example, the hidden labels could be segmentation labels or activation regions in fMRI, while the observable features could be sulcal geometry or MR intensity. We analyze a probabilistic framework for computing an optimal atlas, and the subsequent registration of a new subject using only the observable features to optimize the hidden label alignment to the training set. We compare two approaches for co-registering training images for the atlas construction: the traditional approach of only using observable features and a novel approach of only using hidden labels. We argue that the alternative approach is superior particularly when the relationship between the hidden labels and observable features is complex and unknown. As an application, we consider the task of registering cortical folds to optimize Brodmann area localization. We show that the alignment of the Brodmann areas improves by up to 25% when using the alternative atlas compared with the traditional atlas. To the best of our knowledge, these are the most accurate Brodmann area localization results (achieved via cortical fold registration) reported to date.