1. A method of measuring extent and severity of disease in a patient, comprising the steps of: (a) acquiring a first anatomical image data set and a first functional image data set of the patient, said first anatomical image data set and said first functional image data set form a first co-registered composite image data set; (b) identifying at least a volume of interest (VOI) within said first co-registered composite image data set; (c) qualitatively and quantitatively analyzing said first co-registered composite image data set including said VOI to determine extent and severity of the disease; (d) acquiring a second anatomical image data set and a second functional image data set of the patient, said second anatomical image data set and said second functional image data set form a second co-registered composite image data set; (e) performing a global, rigid registration of said first anatomical image data set and said second anatomical image data set, such that said first functional image data set and said second functional image data set are also globally registered; (f) identifying at least a VOI within the globally registered image data set using the identified VOI within said first co-registered composite image data set; (g) performing a local, non-rigid registration of said VOI within said first co-registered composite image data set and said 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 (h) 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.