Model-based segmentation and analysis of brain images depends on anatomical knowledge which may be derived from conventional atlases. Classical anatomical atlases are based on the rigid spatial distribution provided by a single cadaver. Their use to segment internal anatomical brain structures in a high-resolution MR brain image does not provide any knowledge about the subject variability, and therefore they are not very efficient in analysis. We present a method to develop three-dimensional computerized composite models of brain structures to build a computerized anatomical atlas. The composite models are developed using the real MR brain images of human subjects which are registered through the Principal Axes Transformation. The composite models provide probabilistic spatial distributions, which represent the variability of brain structures and can be easily updated for additional subjects. We demonstrate the use of such a composite model of ventricular structure to help segmentation of the ventricles and Cerebrospinal Fluid (CSF) of MR brain images. In this paper, a composite model of ventricles using a set of 22 human subjects is developed and used in a model-based segmentation of ventricles, sulci, and white matter lesions. To illustrate the clinical usefulness, automatic volumetric measurements on ventricular size and cortical atrophy for an additional eight alcoholics and 10 normal subjects were made. The volumetric quantitative results indicated regional brain atrophy in chronic alcoholics.