The problem of volume averaging in quantitating CSF, gray-matter, and white-matter fractions in the brain is solved using a three-compartment model and a simple graphical analysis of a multispectral MR feature space. Compartmentalization is achieved without the ambiguities of thresholding techniques or the need to assume that the underlying pixel probability distributions have a particular form. A 2D feature space is formed by double SE (proton density- and T2-weighted) MR data with image nonuniformity removed by a novel technique in which the brain itself serves as a uniformity reference. Compartments other than the basic three were rejected by the tailoring of limits in feature space. Phantom scans substantiate this approach, and the importance of the careful selection and standardization of pure tissue reference signals is demonstrated. Compartmental profiles from standardized subvolumes of three normal brains, based on a 3D (Talairach) coordinate system, demonstrate slice-by-slice detail; longitudinal studies confirm reproducibility. Compartmentalization may be described graphically and algebraically, complementing data displays in feature space and images of compartmentalized brain scans. These studies anticipate the application of our compartmentalization technique to patients with neurological disorders.