This paper presents a complete method estimating the displacement field of bodies constrained by an articulated model such as the neck area. Indeed bony structures between different patient images, such as vertebras, may rigidly move while other tissues may deform. The method is divided into 3 steps. The method first registers the articulated rigid bodies together. Then it propagates the deformation into the whole volume through the use of a tetrahedral mesh and it finishes the registration using a mutual information based optical flow. Following the ITK framework, it uses a fast stochastic gradient descent optimization strategy chosen to maximize the mutual information metric. We demonstrate this method provides accurate results on 3D CT, MR and PET images.