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Magnetic resonance imaging (MRI) is an essential tool in the study of muscle anatomy and functional activity in the tongue. Objective assessment of similarities and differences in tongue structure and function has been performed using unnormalised data, but this is biased by the differences in size, shape and orientation of the structures. To remedy this, we propose a methodology to build a 3D vocal tract atlas based on structural MRI volumes from 20 normal subjects. We first constructed high-resolution volumes from three orthogonal stacks. We then removed extraneous data so that all 3D volumes contained the same anatomy. We used an unbiased diffeomorphic groupwise registration using a cross-correlation similarity metric. Principal component analysis was applied to the deformation fields to create a statistical model from the atlas. Various evaluations and applications were carried out to show the behaviour …