In this work, we try to develop a fast converging method for segmentation assisted deformable registration. The segmentation step consists of a piece-wise constant Mumford-Shah energy model while reg- istration is driven by the sum of squared distances of both initial images and segmented mask with a diffusion regularization. In order to solve this energy minimization problem, a second order Gauss-Newton opti- mization method is used. For the numerical experiments we used CT data sets from the EMPIRE10 challenge. In this preliminary study, we show high accuracy of our algorithm.