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We introduce an automated, pathological class level annotation system for medical volumetric brain images. While much of the earlier work has mainly focused on annotating regions of interest in medical images, our system does not require annotated region level training data nor assumes perfect segmentation results for the regions of interest; the time and effort needed for acquiring training data are hence significantly reduced. This capability of handling high-dimensional noisy data, however, poses additional technical challenges, since statistical estimation of models for such data is prone to over-fitting. We propose a framework that combines a regularized logistic regression method and a kernel-based discriminative method to address these problems. Regularized methods provide a flexible selection mechanism that is well-suited for high dimensional noisy data. Our experiments show promising results in classifying computer tomography images of traumatic brain injury patients into pathological classes.