Abstract
Automatic brain tumor segmentation based on 3D mpMRI is highly significant for brain diagnosis, monitoring, and treatment planning. Due to the limitation of manual delineation, automatic and accurate segmentation based on a deep learning network has a tremendous practical necessity. The BraTS2022 challenge provides many data to develop our network. In this work, we proposed a diffraction block based on the Fraunhofer single-slit diffraction principle, which emphasizes the effect of associated features and suppresses isolated features. We added the diffraction block to nn-UNet, which took first place in the BraTS 2020 competition. We also improved nn-UNet by referring to the solution proposed by the 2021 winner, including using a larger network and replacing the batch with a group normalization. In the final unseen test data, our method is ranked first for Pediatric population data and third for BraTS continuous evaluation data.
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References
Rajput, S., Raval, M.S.: A review on end-to-end methods for brain tumor segmentation and overall survival prediction. arXiv preprint arXiv:2006.01632 (2020)
Baid, U., et al.: The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification. arXiv:2107.02314 (2021)
Menze, B.H., Jakab, A., Bauer, S., Kalpathy-Cramer, J., Farahani, K., Kirby, J., et al.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2015). https://doi.org/10.1109/TMI.2014.2377694
Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J.S., et al.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Nat. Sci. Data 4, 170117 (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. The Cancer Imaging Archive (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. The Cancer Imaging Archive (2017). https://doi.org/10.7937/K9/TCIA.2017.GJQ7R0EF
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
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
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
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., Jaeger, P.F., Kohl, S.A., Petersen, J., Maier-Hein, K.H.: nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nat. Methods 18(2), 203–211 (2021)
Luu, H.M., Park, S.H.: Extending nn-UNet for brain tumor segmentation. arXiv preprint arXiv:2112.04653 (2021)
Maji, D., Sigedar, P., Singh, M.: Attention res-UNet with guided decoder for semantic segmentation of brain tumors. Biomed. Signal Process. Control 71, 103077 (2022)
Sun, J., Peng, Y., Guo, Y., Li, D.: Segmentation of the multimodal brain tumor image used the multi-pathway architecture method based on 3D FCN. Neurocomputing 423, 34–45 (2021)
Wang, P., Chung, A.C.: Relax and focus on brain tumor segmentation. Med. Image Anal. 75, 102259 (2022)
Maas, A.L., Hannun, A.Y., Andrew, Y.N.: Rectifier nonlinearities improve neural network acoustic models. Proc. ICML 30(1), 3 (2013)
Ulyanov, D., Vedaldi, A., Lempitsky, V.: Instance normalization: the missing ingredient for fast stylization. arXiv preprint arXiv:1607.08022 (2016)
Milletari, F., Navab, N., Ahmadi, S.A.: V-net: Fully convolutional neural networks for volumetric medical image segmentation. In: International Conference on 3D Vision (3DV), pp. 565–571. IEEE (2016)
Drozdzal, M., Vorontsov, E., Chartrand, G., Kadoury, S., Pal, C.: The importance of skip connections in biomedical image segmentation. Carneiro, G., et al. (eds.) Deep Learning and Data Labeling for Medical Applications, vol. 10008, pp. 179–187. Springer International Publishing Cham (2016). https://doi.org/10.1007/978-3-319-46976-8_19
Wu, Y., He, K.: Group normalization. In: Ferrari, V., Hebert, M., Sminchisescu, C., Weiss, Y. (eds.) ECCV 2018. LNCS, vol. 11217, pp. 3–19. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-01261-8_1
Acknowledgements
We want to acknowledge Fabian Isensee for developing the nn-UNet framework and sharing the models from the 2020 competition and Huan Minh Luu for modifying the nn-UNet and communicating the models from last year’s competition.
This paper is the results of the research project funded by the National Natural Science Foundation of China (61976126) and Shandong Natural Science Foundation (ZR2019MF003).
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Hou, Q., Wang, Z., Wang, J., Jiang, J., Peng, Y. (2023). Diffraction Block in Extended nn-UNet 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_15
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