Genus zero graph segmentation: Estimation of intracranial volume

Rasmus Ramsbøl Jensen, Signe Strann Thorup, Rasmus Reinhold Paulsen, Tron A. Darvann, Nuno V. Hermann, Per Larsen, Sven Kreiborg, Rasmus Larsen

Research output: Contribution to journalJournal articleResearchpeer-review


The intracranial volume (ICV) in children with premature fusion of one or more sutures in the calvaria is of interest due to the risk of increased intracranial pressure. Challenges for automatic estimation of ICV include holes in the skull e.g. the foramen magnum and fontanelles. In this paper, we present a fully automatic 3D graph-based method for segmentation of the ICV in non-contrast CT scans. We reformulate the ICV segmentation problem as an optimal genus 0 segmentation problem in a volumetric graph. The graph is the result of a volumetric spherical subsampling. The equidistantly sampled data points are connected using Delaunay tetrahedralisation creating a highly connected neighborhood. A Markov Random Field (MRF) is constructed on the graph with probabilities learned from an Expectation Maximisation algorithm matching a Mixture of Gaussians to the data. The result of the MRF segmentation is compared to manual segmentations performed by an expert. We have achieved very high Dice scores ranging from 98.14% to 99.00%, while volume deviation from the manual segmentation ranges from 0.7% to 3.7%. The Hausdorff distance, which shows the maximum error from automatic to manual segmentation, ranges from 4.73 to 9.81 mm. Since this is sensitive to single error, we have also found the 95% Hausdorff distance, which ranges from 1.10 to 3.65 mm. The segmentation is very consistent with the reference and differs only in difficult areas, where it seems that our method is much more slice-wise consistent than a manual segmentation. The proposed method is expected to perform well for other volumetric segmentations.
Original languageEnglish
JournalPattern Recognition Letters
Pages (from-to)259-263
Number of pages5
Publication statusPublished - 2014


  • Intracranial volume
  • CT
  • Craniosynostosis
  • Graph cut
  • Markov Random Field
  • Segmentation

Cite this

Jensen, R. R., Thorup, S. S., Paulsen, R. R., Darvann, T. A., Hermann, N. V., Larsen, P., Kreiborg, S., & Larsen, R. (2014). Genus zero graph segmentation: Estimation of intracranial volume. Pattern Recognition Letters, 49, 259-263.