RTK provides the necessary tools to reconstruct an image with motion compensation. The implementation is based on our previous work although it is currently very slow. You should read the following articles to understand the basics of the algorithm:
Rit, S., Sarrut, D. and Desbat, L.
Comparison of analytic and algebraic methods for motion-compensated cone-beam CT reconstruction of the thorax
IEEE Trans Med Imag, 2009, Vol. 28(10), pp. 1513-1525
and
article <a name="rit2009b">(rit2009b)</a>
Rit, S., Wolthaus, J., van Herk, M. and Sonke, J.-J.
On-the-fly motion-compensated cone-beam CT using an a priori model of the respiratory motion
Med Phys, Department of Radiation Oncology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands., 2009, Vol. 36(6), pp. 2283-2296