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A new rigidity penalty was developed to improve the accuracy of an intensity-based B-spline deformable image registration, and its impact on the displacement vector field (DVF) within cervical vertebrae was investigated. The developed rigidity penalty was tested on ten (10) pairs of cone-beam computed tomography (CBCT) scans. The results were compared to those with a conventional rigidity penalty based on the orthonormality of the deformation gradient tensor. The registration error calculated on the DVFs with both penalties was defined as the distance from the ground-truth DVFs obtained by aligning surface models of the pairs of the image data sets. The ability of the image registration methods to cover multiple rigid body motions was evaluated by using orthogonal Procrustes analysis. The results show that the new rigidity penalty better discouraged local deformation within the skeletal components than the conventional orthonormality penalty.