In this work, a new shape based method to improve the accuracy of Brain Ultrasound-MRI image registration is proposed. The method is based on modified Shape Context (SC) descriptor in combination with CPD algorithm. An extensive experiment was carried out to evaluate the robustness of this method against different initialization conditions. As the results prove, the overall performance of the proposed algorithm outperforms both SC and CPD methods. In order to have control over the registration procedure, we simulated the deformations, missing points and outliers according to our Phantom MRI images.