3D variational brain tumor segmentation using Dirichlet priors on a clustered feature set

  • Karteek PopuriEmail author
  • Dana Cobzas
  • Albert Murtha
  • Martin Jägersand
Original Article



Brain tumor segmentation is a required step before any radiation treatment or surgery. When performed manually, segmentation is time consuming and prone to human errors. Therefore, there have been significant efforts to automate the process. But, automatic tumor segmentation from MRI data is a particularly challenging task. Tumors have a large diversity in shape and appearance with intensities overlapping the normal brain tissues. In addition, an expanding tumor can also deflect and deform nearby tissue. In our work, we propose an automatic brain tumor segmentation method that addresses these last two difficult problems.


We use the available MRI modalities (T1, T1c, T2) and their texture characteristics to construct a multidimensional feature set. Then, we extract clusters which provide a compact representation of the essential information in these features. The main idea in this work is to incorporate these clustered features into the 3D variational segmentation framework. In contrast to previous variational approaches, we propose a segmentation method that evolves the contour in a supervised fashion. The segmentation boundary is driven by the learned region statistics in the cluster space. We incorporate prior knowledge about the normal brain tissue appearance during the estimation of these region statistics. In particular, we use a Dirichlet prior that discourages the clusters from the normal brain region to be in the tumor region. This leads to a better disambiguation of the tumor from brain tissue.


We evaluated the performance of our automatic segmentation method on 15 real MRI scans of brain tumor patients, with tumors that are inhomogeneous in appearance, small in size and in proximity to the major structures in the brain. Validation with the expert segmentation labels yielded encouraging results: Jaccard (58%), Precision (81%), Recall (67%), Hausdorff distance (24 mm).


Using priors on the brain/tumor appearance, our proposed automatic 3D variational segmentation method was able to better disambiguate the tumor from the surrounding tissue.


MRI segmentation Variational methods Clustering methods Tumors Edema 


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Copyright information

© CARS 2011

Authors and Affiliations

  • Karteek Popuri
    • 1
    Email author
  • Dana Cobzas
    • 1
  • Albert Murtha
    • 2
  • Martin Jägersand
    • 1
  1. 1.Department of Computing ScienceUniversity of AlbertaEdmontonCanada
  2. 2.Department of OncologyUniversity of AlbertaEdmontonCanada

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