This paper introduces a new registration method estimating the displacement field of bodies which deformations are constrained by an articulated rigid body. We propose an articulated transformation model embedded in a general registration scheme. A fast stochastic gradient descent optimization strategy suitable for noisy cost functions has been chosen to maximize the mutual information metric. Once registered, we propose to propagate the deformation by a linear elastic model through the use of a tetrahedral mesh. We demonstrate this method on 3D CT of neck images where bony structures between different patient images, as vertebrae, may rigidly move while other tissues may deform.