This paper introduces a new method for automatic quantification of subcutaneous, visceral and nonvisceral internal fat from MR-images acquired using the two point Dixon technique in the abdominal region. The method includes (1) a three dimensional phase unwrapping to provide water and fat images, (2) an image intensity inhomogeneity correction, and (3) a morphon based registration and segmentation of the tissue. This is followed by an integration of the corrected fat images within the different fat compartments that avoids the partial volume effects associated with traditional fat segmentation methods. The method was tested on 18 subjects before and after a period of fastfood hyper-alimentation showing high stability and performance in all analysis steps.