A combined interpolation – three-dimensional level set method (3D LSM)-based segmentation process is presented. The performance in terms of accuracy of the 3D LSM in the segmentation of throat regions from highly anisotropic magnetic resonance imaging (MRI) volumes, with and without an interpolation step is evaluated. Qualitative and quantitative results from real MRI data suggest that performing interpolation, to reconstruct isotropic MRI volumes, prior to 3D LSM improves the accuracy of the segmentation results, compared to interpolation post 3D LSM and no interpolation at all.