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This paper presents a novel free-form deformation registration algorithm with non-rigid constraints to capture the transformation between the planning day and treatment day CT images used for external beam radiotherapy for prostate cancer. The algorithm is constrained to the predetermined motion of a segmented organ, which is described by an injective free-form deformation (FFD) based on B-splines. The end goal is for the injective transformation to be used to update the radiotherapy plan to take into account bone and soft tissue deformation. The results of the algorithm have been compared to those achieved using rigid and fully non-rigid registration. The results clearly indicate that the constrained non-rigid registration algorithm presented in this paper performed much better at capturing the motion of the constrained organ, the bladder in this case, than the rigid or fully non-rigid registration algorithms.