1. A system for measuring extent and severity of disease in a patient, comprising: an imaging device for acquiring a plurality of anatomical image data sets and a plurality of functional image data sets of the patient, said plurality of anatomical image data sets and said plurality of functional image data sets form a plurality of co-registered composite image data sets; a user device for identifying at least a volume of interest (VOI) within a co-registered composite image data set of said plurality of co-registered composite image data sets, and identifying at least a VOI within a globally registered image data set of a plurality of globally registered image data sets using the identified VOI within said co-registered composite image data set; and a computer system for performing the following steps: qualitatively and quantitatively analyzing a first co-registered composite image data set of said plurality of co-registered composite image data sets including the identified VOI to determine extent and severity of the disease; performing a global, rigid registration of a first anatomical image data set and a second anatomical image data set of said plurality of anatomical image data sets, such that a first functional image data set and a second functional image data set of said plurality of functional image data sets are also globally registered; performing a local, non-rigid registration of the VOI within said first co-registered composite image data set and the VOI within the globally registered image data set, thereby producing a first co-registered serial image data set, said local, non-rigid registration being more precise than said global, rigid registration; and qualitatively and quantitatively analyzing said first co-registered serial image data set including the VOIs to determine severity of the disease and/or response to treatment of the patient.