Radiation induced pulmonary diseases can change the tissue material properties of lung parenchyma and the mechanics of the respiratory system. Recent advances in multi-detector-row CT (MDCT), 4DCT respiratory gating methods, and image processing techniques enable us to follow and measure those changes noninvasively during radiation therapy at a regional level. This study compares the 4DCT based ventilation measurement with the results from hyperpolarized helium-3 MR using the cumulative distribution function maps and the relative overlap (RO) statistic. We show that the similarity between the two measurements increases as the increase of the B-Spline grid spacing and Laplacian weighting which result a smoother ventilation map. The best similarity is found with weighting of 0.5 for linear elasticity and B-Spline grid spacing of 32 mm. Future work is to improve the lung image registration algorithm by incorporating hyperpolarized helium-3 MR information so as to improve its physiological modeling of the lung tissue deformation.