Tracking of signal intensity changes in soft tissue over time is often hampered by deformation of the tissue. In this study a method is described that uses finite element modeling to compensate for tissue deformation. The method is applied to the quantification of fluid redistribution in an intervertebral disc that deforms under mechanical load. The clinical importance of this application emerges from the increased susceptibility of the intervertebral disc to damage after a period of mechanical loading. The study shows that the use of the finite element aided approach results in a detailed map of tissue MRI signal changes, where the distorting effects of tissue deformation are eliminated.