We present an automatic method for selecting regions of interest (ROIs) of the information contained in three-dimensional functional brain images using Gaussian mixture models (GMMs), where each Gaussian incorporates a contiguous brain region with similar activation. The novelty of the approach is based on approximating the grey-level distribution of a brain image by a sum of Gaussian functions, whose parameters are determined by a maximum likelihood criterion via the expectation maximization (EM) algorithm. Each Gaussian or cluster is represented by a multivariate Gaussian function with a center coordinate and a certain shape. This approach leads to a drastic compression of the information contained in the brain image and serves as a starting point for a variety of possible feature extraction methods for the diagnosis of brain diseases.