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Deformable image registration of four head and neck cancer patients has been conducted using a biomechanical-based model. Patient-specific 3D finite element models have been developed using CT and cone-beam CT image data of the planning and a radiation treatment session. The model consists of seven vertebrae (C1 to C7), mandible, larynx, left and right parotid glands, tumor and body. Different combinations of boundary conditions are applied in the model in order to find the configuration with a minimum registration error. Each vertebra in the planning session is individually aligned with its correspondence in the treatment session. Rigid alignment is used for each individual vertebra and the mandible since no deformation is expected in the bones. In addition, the effect of morphological differences in the external body between the two image sessions is investigated. The accuracy of the registration is evaluated using the tumor and both parotid glands by comparing the calculated Dice similarity index of these structures following deformation in relation to their true surface defined in the image of the second session. The registration is improved when the vertebrae and mandible are aligned in the two sessions with the highest average Dice index of 0.86 +- 0.08, 0.84 +- 0.11 and 0.89 +- 0.04 for the tumor, left and right parotid glands, respectively. The accuracy of the center of mass location of tumor and parotid glands is also improved by deformable image registration where the errors in the tumor and parotid glands decrease from 4.0 +- 1.1, 3.4 +- 1.5 and 3.8 +- 0.9 mm using rigid registration to 2.3 +- 1.0, 2.5 +- 0.8 and 2.0 +- 0.9 mm in the deformable image registration when alignment of vertebrae and mandible is conducted in addition to the surface projection of the body. [ABSTRACT FROM AUTHOR]