A method and system for measuring disease relevant tissue changes for use in quantifying, diagnosing and predicting a given disease are provided. The method comprises applying at least one segmenting process to the image data to generate a plurality of segmented regions of interest, extracting features relevant for a given disease from the segmented regions to generate extracted features, and mathematically modeling the features for use in one of diagnosing, quantifying and predicting changes indicative of the given disease. The system comprises an imaging device for acquiring the image data and an image process configured to segment, extract and mathematically model disease relevant features.