Abstract
Segmentation of brain tumors from multiple MRI modalities is necessary for successful disease diagnosis and clinical treatment. In recent years, Transformer-based networks with the self-attention mechanism have been proposed. But they do not show the performance beyond the U-shaped fully convolutional network. In this paper, we apply HFTrans network to the brain tumor segmentation task of BraTS 2022 challenge by focusing on the multi-modalities of MRI with the benefits of Transformer. By applying BraTS-specific modifications of preprocessing, aggressive data augmentation, and postprocessing, our method shows superior results in comparisons between previous best performers. We show that the final result on the BraTS 2022 validation dataset achieves dice scores of 82.94%, 85.48%, and 92.44% and Hausdorff distances of 14.55 mm, 12.96 mm, and 3.77 mm for enhancing tumor, tumor core, and whole tumor, respectively.
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References
Bakas, S., et al.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-GBM collection (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 (2017). https://doi.org/10.7937/K9/TCIA.2017.GJQ7R0EF
Bakas, S., et al.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4(1), 1–13 (2017)
Bakas, S., 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)
Chen, J., et al.: Transunet: transformers make strong encoders for medical image segmentation. arXiv preprint arXiv:2102.04306 (2021)
Cho, J., Park, J.: Hybrid-fusion transformer for multisequence MRI. In: Medical Imaging and Computer-Aided Diagnosis. Springer, Cham (2022, in press)
Dosovitskiy, A., et al.: An image is worth 16x16 words: transformers for image recognition at scale. arXiv preprint arXiv:2010.11929 (2020)
Hatamizadeh, A., Nath, V., Tang, Y., Yang, D., Roth, H., Xu, D.: Swin UNETR: swin transformers for semantic segmentation of brain tumors in MRI images. arXiv preprint arXiv:2201.01266 (2022)
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
Isensee, F., et al.: nnu-net: self-adapting framework for u-net-based medical image segmentation. arXiv preprint arXiv:1809.10486 (2018)
Long, J., Shelhamer, E., Darrell, T.: Fully convolutional networks for semantic segmentation. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 3431–3440 (2015)
Luu, H.M., Park, S.H.: Extending nn-unet for brain tumor segmentation. arXiv preprint arXiv:2112.04653 (2021)
Menze, B.H., et al.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2014)
Milletari, F., Navab, N., Ahmadi, S.A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: 2016 Fourth International Conference on 3D Vision (3DV), pp. 565–571. IEEE (2016)
Pérez-García, F., Sparks, R., Ourselin, S.: Torchio: a python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning. Comput. Methods Programs Biomed. 106236 (2021). https://doi.org/10.1016/j.cmpb.2021.106236. https://www.sciencedirect.com/science/article/pii/S0169260721003102
Ronneberger, O., Fischer, P., Brox, T.: U-net: convolutional networks for biomedical image segmentation. CoRR abs/1505.04597 (2015). http://arxiv.org/abs/1505.04597
Wang, W., Chen, C., Ding, M., Yu, H., Zha, S., Li, J.: TransBTS: multimodal brain tumor segmentation using transformer. In: de Bruijne, M., et al. (eds.) MICCAI 2021. LNCS, vol. 12901, pp. 109–119. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-87193-2_11
Acknowledgements
This research was supported by the Capacity Enhancement Program for Scientific and Cultural Exhibition Services through the National Research Foundation of Korea (NRF) funded by Ministry of Science and ICT (No. NRF-2018X1A3A1069693) and Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government (MOTIE) (20201510300280, Development of a remote dismantling training system with force-torque responding virtual nuclear power plant).
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Cho, J., Park, J. (2023). Multi-modal Transformer for Brain Tumor Segmentation. In: Bakas, S., et al. Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2022. Lecture Notes in Computer Science, vol 13769. Springer, Cham. https://doi.org/10.1007/978-3-031-33842-7_12
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DOI: https://doi.org/10.1007/978-3-031-33842-7_12
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