Abstract
In this paper we described our approach for glioma segmentation in multi-sequence magnetic resonance imaging (MRI) in the context of the MICCAI 2020 Brain Tumor Segmentation Challenge (BraTS). We proposed an architecture based on U-Net with a new computational unit termed “SE Norm” that brought significant improvements in segmentation quality. Our approach obtained competitive results on the validation (Dice scores of 0.780, 0.911, 0.863) and test (Dice scores of 0.805, 0.887, 0.843) sets for the enhanced tumor, whole tumor and tumor core sub-regions. The full implementation and trained models are available at https://github.com/iantsen/brats.
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References
Bakas, S.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Nature Sci. Data 4(1), 1–13 (2017)
Upadhyay, N., Waldman, A.: Conventional MRI evaluation of gliomas. British J. Radiol. 84(2), Special Issue 2 S107–S111 (2011)
Menze, B.H., et al.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2015)
Bakas, S. et al: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-GBM collection. TCIA (2017)
Bakas, S., et al.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-LGG collection. TCIA (2017)
Bakas, S., Reyes, M., Jakab, A., Bauer, S., Rempfler, M., Crimi, A. et al.: Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge. arXiv preprint arXiv:1811.02629 (2018)
Ioffe, S., Szegedy, C.: Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift. arXiv preprint arXiv:1502.03167 (2015)
Ulyanov, D., Vedaldi, A., Lempitsky, V.: Instance normalization: The missing ingredient for fast stylization. arXiv preprint arXiv:1607.08022 (2016)
Ba, J.L., Kiros, J.R., Hinton, G.E.: Layer Normalization. arXiv preprint arXiv:1607.06450 (2016)
Wu, Y., He, K.: Group normalization. In: European Conference on Computer Vision (ECCV) (2018)
Hu, J., Shen, L., Sun, G.: Squeeze-and-excitation networks, CoRR, vol. abs/1709.01507 (2017). http://arxiv.org/abs/1709.01507
Ronneberger, O., Fischer, P., Brox, T.: U-net: convolutional networks for biomedical image segmentation. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9351, pp. 234–241. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-24574-4_28
Çiçek, Ö., Abdulkadir, A., Lienkamp, S.S., Brox, T., Ronneberger, O.: 3D U-net: learning dense volumetric segmentation from sparse annotation. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016. LNCS, vol. 9901, pp. 424–432. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46723-8_49
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
Tompson, J., Goroshin, R., Jain, A., LeCun, Y., Bregler, C.: Efficient Object Localization Using Convolutional Networks. arXiv preprint arXiv:1411.4280 (2014)
Milletari, F., Navab, N., Ahmadi, S.-A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: International Conference on 3D Vision, pp. 565–571. IEEE (2016)
Lin, T.-Y., Goyal, P., Girshick, R., He, K., Dollár, P.: Focal Loss for Dense Object Detection. arXiv preprint arXiv:1708.02002 (2017)
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Iantsen, A., Jaouen, V., Visvikis, D., Hatt, M. (2021). Squeeze-and-Excitation Normalization for Brain Tumor Segmentation. In: Crimi, A., Bakas, S. (eds) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2020. Lecture Notes in Computer Science(), vol 12659. Springer, Cham. https://doi.org/10.1007/978-3-030-72087-2_32
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