Abstract
Gliomas are brain tumors originating from the neuronal support tissue called glia, which can be benign or malignant. They are considered rare tumors, whose prognosis, which is highly fluctuating, is primarily related to several factors, including localization, size, degree of extension and certain immune factors. We propose an approach using a Residual 3D U-Net to segment these tumors with localization, a technique for centering and reducing the size of input images to make more accurate and faster predictions. We incorporated different training and post-processing techniques such as cross-validation and minimum pixel threshold.
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References
Abraham, N., Khan, N.: A novel focal Tversky loss function with improved attention u-net for lesion segmentation. In: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), pp. 683–687 (2019)
Baid, U., et al.: The RSNA-ASNR-MICCAI BraTs 2021 benchmark on brain tumor segmentation and radiogenomic classification. CoRR abs/2107.02314 (2021). https://arxiv.org/abs/2107.02314
Bakas, S., et al.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4 (2017). https://doi.org/10.1038/sdata.2017.117
Bakas, S., et al.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-GBM collection, July 2017. https://doi.org/10.7937/K9/TCIA.2017.KLXWJJ1Q
Bakas, S., et al.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-LGG collection, July 2017. https://doi.org/10.7937/K9/TCIA.2017.GJQ7R0EF
Caesar, H., Uijlings, J.R.R., Ferrari, V.: Region-based semantic segmentation with end-to-end training (2016). http://arxiv.org/abs/1607.07671
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
Eelbode, T., et al.: Optimization for medical image segmentation: theory and practice when evaluating with dice score or Jaccard index. IEEE Trans. Med. Imaging 39(11), 3679–3690 (2020). https://doi.org/10.1109/TMI.2020.3002417
Fidon, L., et al.: Generalised Wasserstein dice score for imbalanced multi-class segmentation using holistic convolutional networks. In: Crimi, A., Bakas, S., Kuijf, H., Menze, B., Reyes, M. (eds.) BrainLes 2017. LNCS, vol. 10670, pp. 64–76. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-75238-9_6
Guo, D., Wang, L., Song, T., Wang, G.: Cascaded global context convolutional neural network for brain tumor segmentation. In: Crimi, A., Bakas, S. (eds.) BrainLes 2019. LNCS, vol. 11992, pp. 315–326. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-46640-4_30
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
Isensee, F., Jäger, P.F., Full, P.M., Vollmuth, P., Maier-Hein, K.H.: nnU-Net for brain tumor segmentation. In: Crimi, A., Bakas, S. (eds.) BrainLes 2020. LNCS, vol. 12659, pp. 118–132. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-72087-2_11
Islam, M., Vibashan, V.S., Jose, V.J.M., Wijethilake, N., Utkarsh, U., Ren, H.: Brain tumor segmentation and survival prediction using 3D attention UNet. In: Crimi, A., Bakas, S. (eds.) BrainLes 2019. LNCS, vol. 11992, pp. 262–272. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-46640-4_25
Jiang, Z., Ding, C., Liu, M., Tao, D.: Two-stage cascaded U-net: 1st place solution to BraTS challenge 2019 segmentation task. In: Crimi, A., Bakas, S. (eds.) BrainLes 2019. LNCS, vol. 11992, pp. 231–241. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-46640-4_22
Lee, C.Y., Xie, S., Gallagher, P., Zhang, Z., Tu, Z.: Deeply-supervised nets. In: Lebanon, G., Vishwanathan, S.V.N. (eds.) Proceedings of the Eighteenth International Conference on Artificial Intelligence and Statistics. Proceedings of Machine Learning Research, vol. 38, pp. 562–570. PMLR, San Diego, California, USA, 09–12 May 2015. http://proceedings.mlr.press/v38/lee15a.html
Lee, K., Zung, J., Li, P., Jain, V., Seung, H.: Superhuman accuracy on the snemi3D connectomics challenge. arXiv abs/1706.00120 (2017)
Menze, B.H., et al.: The multimodal brain tumor image segmentation benchmark BbraTs). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2015). https://doi.org/10.1109/TMI.2014.2377694
Milletari, F., Navab, N., Ahmadi, S.A.: V-net: fully convolutional neural networks for volumetric medical image segmentation (2016)
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
Yu, L., Yang, X., Chen, H., Qin, J., Heng, P.A.: Volumetric convnets with mixed residual connections for automated prostate segmentation from 3D MR images, January 2017
Zhao, Y.-X., Zhang, Y.-M., Liu, C.-L.: Bag of tricks for 3D MRI brain tumor segmentation. In: Crimi, A., Bakas, S. (eds.) BrainLes 2019. LNCS, vol. 11992, pp. 210–220. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-46640-4_20
Acknowledgement
We would like to thank Arnaud Renard and his team, for the access to their supercomputer ROMEO, the Regional Super Computer Center hosted by the University of Reims Champagne-Ardenne. We also would like to thank Christian Chabrerie for his support throughout the project.
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Demoustier, M., Khemir, I., Nguyen, Q.D., Martin-Gaffé, L., Boutry, N. (2022). Residual 3D U-Net with Localization for Brain Tumor Segmentation. In: Crimi, A., Bakas, S. (eds) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2021. Lecture Notes in Computer Science, vol 12962. Springer, Cham. https://doi.org/10.1007/978-3-031-08999-2_33
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