MRI is a valuable tool in the diagnosis of multiple sclerosis (MS). Standard MR protocols for imaging MS produce proton density (PD) and T2 weighted images of the same slice in the brain. While these image pairs provide valuable information about MS lesions, they are two dimensional (2-D) while lesions are three dimensional (3-D). Furthermore, the vast amount of data produced in an MR exam for MS makes routine analysis and comparison of the image pairs difficult. Therefore, we have developed a computerized system which employs multi-spectral analysis techniques to allow interactive 3-D analysis of MR data by radiologists and neurologists. We have used our system to classify and analyze four MR exams of a chronic-progressive MS patient taken over an 18 month period. Comparison of volume renderings of classified white matter, grey matter and MS lesions at each exam date provide information about the changes in individual lesions, and total lesion burden. Analysis of the intensity distributions of large MS lesions reveals that they have a wide range of PD/T2 weighted intensities, and some contain a higher PD/longer T2 'core' perhaps corresponding to edema.