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Robust Semantic Segmentation of Brain Tumor Regions from 3D MRIs

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Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries (BrainLes 2019)

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Abstract

Multimodal brain tumor segmentation challenge (BraTS) brings together researchers to improve automated methods for 3D MRI brain tumor segmentation. Tumor segmentation is one of the fundamental vision tasks necessary for diagnosis and treatment planning of the disease. Previous years winning methods were all deep-learning based, thanks to the advent of modern GPUs, which allow fast optimization of deep convolutional neural network architectures. In this work, we explore best practices of 3D semantic segmentation, including conventional encoder-decoder architecture, as well combined loss functions, in attempt to further improve the segmentation accuracy. We evaluate the method on BraTS 2019 challenge.

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References

  1. Bakas, S., et al.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-GBM collection. The Cancer Imaging Archive (2017). https://doi.org/10.7937/K9/TCIA.2017.KLXWJJ1Q

  2. Bakas, S., et al.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-LGG collection. The Cancer Imaging Archive (2017). https://doi.org/10.7937/K9/TCIA.2017.GJQ7R0EF

  3. Bakas, S., Akbari, H., et al.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4, 170117 (2017)

    Article  Google Scholar 

  4. Bakas, S., Reyes, M., et Int, Menze, B.: Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge. arXiv:1811.02629 (2018)

  5. Chen, L.C., Zhu, Y., Papandreou, G., Schroff, F., Adam, H.: Encoder-decoder with atrous separable convolution for semantic image segmentation. arXiv:1802.02611 (2018)

  6. Chen, X., Williams, B.M., Vallabhaneni, S.R., Czanner, G., Williams, R., Zheng, Y.: Learning active contour models for medical image segmentation. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 11632–11640 (2019)

    Google Scholar 

  7. Hatamizadeh, A., Sengupta, D., Terzopoulos, D.: End-to-end deep convolutional active contours for image segmentation. arXiv preprint arXiv:1909.13359 (2019)

  8. He, K., Zhang, X., Ren, S., Sun, J.: Identity mappings in deep residual networks. In: Leibe, B., Matas, J., Sebe, N., Welling, M. (eds.) ECCV 2016. LNCS, vol. 9908, pp. 630–645. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46493-0_38

    Chapter  Google Scholar 

  9. Huang, G., Liu, Z., van der Maaten, L., Weinberger, K.Q.: Densely connected convolutional networks. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 2261–2269 (2017)

    Google Scholar 

  10. Ioffe, S., Szegedy, C.: Batch normalization: Accelerating deep network training by reducing internal covariate shift. In: International Conference on Machine Learning (ICML), pp. 448–456 (2015)

    Google Scholar 

  11. Isensee, F., Kickingereder, P., Wick, W., Bendszus, M., Maier-Hein, K.H.: No new-net. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 234–244. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_21

    Chapter  Google Scholar 

  12. Lin, T.Y., Goyal, P., Girshick, R., He, K., Dollár, P.: Focal loss for dense object detection. In: Proceedings of the IEEE international conference on computer vision, pp. 2980–2988 (2017)

    Google Scholar 

  13. McKinley, R., Meier, R., Wiest, R.: Ensembles of densely-connected CNNs with label-uncertainty for brain tumor segmentation. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 456–465. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_40

    Chapter  Google Scholar 

  14. Menze, B.H., et al.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2015)

    Article  Google Scholar 

  15. Milletari, F., Navab, N., Ahmadi, S.A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: Fourth International Conference on 3D Vision (3DV) (2016)

    Google Scholar 

  16. Myronenko, A.: 3D MRI brain tumor segmentation using autoencoder regularization. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 311–320. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_28

    Chapter  Google Scholar 

  17. Ulyanov, D., Vedaldi, A., Lempitsky, V.S.: Instance normalization: the missing ingredient for fast stylization. In: CVPR (2016)

    Google Scholar 

  18. Wu, Y., He, K.: Group normalization. In: European Conference on Computer Vision (ECCV) (2018)

    Google Scholar 

  19. Zhou, C., Chen, S., Ding, C., Tao, D.: Learning contextual and attentive information for brain tumor segmentation. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 497–507. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_44

    Chapter  Google Scholar 

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Correspondence to Andriy Myronenko .

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Myronenko, A., Hatamizadeh, A. (2020). Robust Semantic Segmentation of Brain Tumor Regions from 3D MRIs. In: Crimi, A., Bakas, S. (eds) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2019. Lecture Notes in Computer Science(), vol 11993. Springer, Cham. https://doi.org/10.1007/978-3-030-46643-5_8

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  • DOI: https://doi.org/10.1007/978-3-030-46643-5_8

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