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Brain tumor detection and segmentation in a CRF (conditional random fields) framework with pixel-pairwise affinity and superpixel-level features

Abstract

Purpose

Detection and segmentation of a brain tumor such as glioblastoma multiforme (GBM) in magnetic resonance (MR) images are often challenging due to its intrinsically heterogeneous signal characteristics. A robust segmentation method for brain tumor MRI scans was developed and tested.

Methods

Simple thresholds and statistical methods are unable to adequately segment the various elements of the GBM, such as local contrast enhancement, necrosis, and edema. Most voxel-based methods cannot achieve satisfactory results in larger data sets, and the methods based on generative or discriminative models have intrinsic limitations during application, such as small sample set learning and transfer. A new method was developed to overcome these challenges. Multimodal MR images are segmented into superpixels using algorithms to alleviate the sampling issue and to improve the sample representativeness. Next, features were extracted from the superpixels using multi-level Gabor wavelet filters. Based on the features, a support vector machine (SVM) model and an affinity metric model for tumors were trained to overcome the limitations of previous generative models. Based on the output of the SVM and spatial affinity models, conditional random fields theory was applied to segment the tumor in a maximum a posteriori fashion given the smoothness prior defined by our affinity model. Finally, labeling noise was removed using “structural knowledge” such as the symmetrical and continuous characteristics of the tumor in spatial domain.

Results

The system was evaluated with 20 GBM cases and the BraTS challenge data set. Dice coefficients were computed, and the results were highly consistent with those reported by Zikic et al. (MICCAI 2012, Lecture notes in computer science. vol 7512, pp 369–376, 2012).

Conclusion

A brain tumor segmentation method using model-aware affinity demonstrates comparable performance with other state-of-the art algorithms.

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Acknowledgments

This work was partially supported by the Chinese National Science Foundation (61273241) and the NSF CAREER grant IIS-0845282. Conflict of Interest   The authors have declared that no conflict of interest exists.

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Correspondence to Wei Wu.

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Wu, W., Chen, A.Y.C., Zhao, L. et al. Brain tumor detection and segmentation in a CRF (conditional random fields) framework with pixel-pairwise affinity and superpixel-level features. Int J CARS 9, 241–253 (2014). https://doi.org/10.1007/s11548-013-0922-7

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Keywords

  • Brain tumor segmentation
  • Model-aware affinity
  • SVM
  • CRF
  • Superpixels