Abstract
A deep learning method is proposed for brain tumor segmentation using a two-stage encoder-decoder convolutional neural network (CNN). To improve the generalization of the proposed network for federated evaluation, we propose a two-stage encoder-decoder CNN that performs coarse segmentation at stage-I and fine segmentation at stage-II. Stage-I consists of an ensemble of three predictions on the orthogonal slices of a subject. In stage-II, the predictions of the first stage are used to crop the region of interest consisting of the tumor region and a fine grain segmentation is performed on the cropped image. A single ResUNet was used for stage-I and seven different networks were used for stage-II. Heavy data augmentation consisting of geometric transformation and random contrast was used to avoid overfitting and improve the generalization. The mean dice scores on 21 imaging sites evaluated in a federated manner achieved dice scores of 0.8659, 0.7708, and 0.7714 for the whole tumor, tumor core, and enhancing tumor respectively. The method ranked second in the federated evaluation task.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
Notes
- 1.
code repository: https://github.com/kamleshpawar17/FeTS2021
References
Mazzara, G.P., Velthuizen, R.P., Pearlman, J.L., Greenberg, H.M., Wagner, H.: Brain tumor target volume determination for radiation treatment planning through automated MRI segmentation. Int. J. Radiation Oncol. Biol. Phys. 59, 300–312 (2004)
Bakas, S., et al.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Scientific Data 4, 170117 (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)
Bakas, S., et al.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-LGG collection. The Cancer Imaging Archive 286 (2017)
Menze, B.H., et al.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imag. 34(10), 1993 (2015)
Pati, S., et al.: The federated tumor segmentation (FeTS) challenge. arXiv preprint arXiv:2105.05874 (2021)
Reina, G.A., et al.: OpenFL: An open-source framework for Federated Learning. arXiv preprint arXiv:2105.06413 (2021)
LeCun, Y.A., Bengio, Y., Hinton, G.E.: Deep learning. Nature 521, 436–444 (2015)
Pawar, K., Zhaolin Chen, N., Shah, J., Egan, G.F.: An ensemble of 2D convolutional neural network for 3D brain tumor segmentation. In: Crimi, Alessandro, Bakas, Spyridon (eds.) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: 5th International Workshop, BrainLes 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 17, 2019, Revised Selected Papers, Part I, pp. 359–367. Springer International Publishing, Cham (2020). https://doi.org/10.1007/978-3-030-46640-4_34
Pawar, K., Chen, Z., Shah, N.J., Egan, G.: Residual encoder and convolutional decoder neural network for glioma segmentation. In: Crimi, A., Bakas, S., Kuijf, H., Menze, B., Reyes, M. (eds.) BrainLes 2017. LNCS, vol. 10670, pp. 263–273. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-75238-9_23
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
Zhou, Z., Siddiquee, M.M.R., Tajbakhsh, N., Liang, J.: Unet++: a nested u-net architecture for medical image segmentation. In: Deep learning in medical image analysis and multimodal learning for clinical decision support, pp. 3–11. Springer (2018)
Lin, T.-Y., Dollár, P., Girshick, R., He, K., Hariharan, B., Belongie, S.: Feature pyramid networks for object detection. In: Proceedings of the IEEE conference on computer vision and pattern recognition, pp. 2117–2125 (2017)
He, K.M., Zhang, X.Y., Ren, S.Q., Sun, J.: Deep Residual Learning for Image Recognition. Proc Cvpr Ieee 770–778 (2016)
Chen, Y., Li, J., Xiao, H., Jin, X., Yan, S., Feng, J.: Dual path networks. arXiv preprint arXiv:1707.01629 (2017)
Szegedy, C., Ioffe, S., Vanhoucke, V., Alemi, A.A.: Inception-v4, inception-resnet and the impact of residual connections on learning. In: Thirty-First AAAI Conference on Artificial Intelligence (2017)
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. 4700–4708 (2017)
Tan, M., Le, Q.: Efficientnet: rethinking model scaling for convolutional neural networks. In: International Conference on Machine Learning, pp. 6105–6114. PMLR
Yakubovskiy, P.: Segmentation Models Pytorch. GitHub Repository (2020). https://github.com/qubvel/segmentation_models.pytorch
Smith, L.N.: Cyclical learning rates for training neural networks. In: 2017 IEEE winter conference on applications of computer vision (WACV), pp. 464–472. IEEE (2017)
Wu, K., Otoo, E., Shoshani, A.: Optimizing connected component labeling algorithms. In: Medical Imaging 2005: Image Processing, vol. 5747, pp. 1965–1976. SPIE (2005)
Deng, J., Dong, W., Socher, R., Li, L.-J., Li, K., Fei-Fei, L.: Imagenet: a large-scale hierarchical image database. In: 2009 IEEE conference on computer vision and pattern recognition, pp. 248–255. IEEE (2009)
Alzubaidi, L., Fadhel, M.A., Al-Shamma, O., Jinglan Zhang, J., Santamaría, Y.D., Oleiwi, S.R.: Towards a better understanding of transfer learning for medical imaging: a case study. Appl. Sci. 10(13), 4523 (2020)
Pawar, K., Chen, Z., Shah, N.J., Egan, G.F.: A deep learning framework for transforming image reconstruction into pixel classification. IEEE Access 7, 177690–177702 (2019)
Pawar, K., Zhaolin Chen, N., Shah, J., Egan, G.F.: Suppressing motion artefacts in MRI using an Inception‐ResNet network with motion simulation augmentation. NMR Biomed. 35(4), e4225 (2019). https://doi.org/10.1002/nbm.4225
Pawar, K., Egan, G.F., Chen, Z.: Domain knowledge augmentation of parallel MR image reconstruction using deep learning. Comput, Med. Imaging Graphics 92, 101968 (2021). https://doi.org/10.1016/j.compmedimag.2021.101968
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this paper
Cite this paper
Pawar, K., Zhong, S., Chen, Z., Egan, G. (2022). Brain Tumor Segmentation Using Two-Stage Convolutional Neural Network for Federated Evaluation. In: Crimi, A., Bakas, S. (eds) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2021. Lecture Notes in Computer Science, vol 12963. Springer, Cham. https://doi.org/10.1007/978-3-031-09002-8_43
Download citation
DOI: https://doi.org/10.1007/978-3-031-09002-8_43
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-09001-1
Online ISBN: 978-3-031-09002-8
eBook Packages: Computer ScienceComputer Science (R0)