A hybrid calibration method uses an calibration phantom (exterior reference) scanned simultaneously with the patient, and one or more known tissues of the subject (interior reference) to create a hybrid calibration reference that improves the measurement of tissue densities throughout the body. In addition, the calibration method is used to quantitatively define boundaries of tissue and organs for more accurate measurements of lengths, areas and volumes. Another aspect of the invention uses the calibrated images to quantitatively preset absolute window/levels for filming and image display, which provides standardized viewing for diagnostic purposes.