For diagnosis, preoperative planning and postoperative guides, an accurate estimate of joints kinematics is required. We bring together MRI developments and new image processing methods in order to automatically extract active bone kinematics from multi-slice real-time dynamic MRI. We introduce a tracking algorithm based on 2D/3D registration and a procedure to validate the technique by using both dynamic and sequential MRI. We present how we optimize jointly the tracking method and the acquisition protocol to overcome the trade-off in acquisition time and tracking accuracy. As a case study, we apply this methodology on the human hip joint.