Automated segmentation of mouse brain images using extended MRF

Min Hyeok Bae, Rong Pan, Teresa Wu, Alexandra Badea

Research output: Contribution to journalArticlepeer-review

43 Scopus citations


We introduce an automated segmentation method, extended Markov random field (eMRF), to classify 21 neuroanatomical structures of mouse brain based on three dimensional (3D) magnetic resonance images (MRI). The image data are multispectral: T2-weighted, proton density-weighted, diffusion x, y and z weighted. Earlier research (Ali, A.A., Dale, A.M., Badea, A., Johnson, G.A., 2005. Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. NeuroImage 27 (2), 425-435) successfully explored the use of MRF for mouse brain segmentation. In this research, we study the use of information generated from support vector machine (SVM) to represent the probabilistic information. Since SVM in general has a stronger discriminative power than the Gaussian likelihood method and is able to handle nonlinear classification problems, integrating SVM into MRF improved the classification accuracy. The eMRF employs the posterior probability distribution obtained from SVM to generate a classification based on the MR intensity. Secondly, the eMRF introduces a new potential function based on location information. Third, to maximize the classification performance, the eMRF uses the contribution weights optimally determined for each of the three potential functions: observation, location and contextual functions, which are traditionally equally weighted. We use the voxel overlap percentage and volume difference percentage to evaluate the accuracy of eMRF segmentation and compare the algorithm with three other segmentation methods - mixed ratio sampling SVM (MRS-SVM), atlas-based segmentation and MRF. Validation using classification accuracy indices between automatically segmented and manually traced data shows that eMRF outperforms other methods.

Original languageEnglish (US)
Pages (from-to)717-725
Number of pages9
Issue number3
StatePublished - Jul 1 2009


  • Automated segmentation
  • Data mining
  • Magnetic resonance microscopy
  • Markov random field
  • Mouse brain
  • Support vector machine

ASJC Scopus subject areas

  • Neurology
  • Cognitive Neuroscience


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