Skip to main content

An Empirical Study of Deep Neural Networks for Glioma Detection from MRI Sequences

  • Conference paper
  • First Online:

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 12532))

Abstract

Gliomas are the most common central nervous system tumors. They represent 1.3% of cancers and are the 15th most common cancer for men and women. For the diagnosis of such pathology, doctors commonly use Magnetic Resonance Imaging (MRI) with different sequences. In this work, we propose a global framework using convolutional neural networks to create an intelligent assistant system for neurologists to diagnose the brain gliomas. Within this framework, we study the performance of different neural networks on four MRI modalities. This work allows us to highlight the most specific MRI sequences so that the presence of gliomas in brain tissue can be classified. We also visually analyze extracted features from the different modalities and networks with an aim to improve the interpretability and analysis of the performance obtained. We apply our study on the MRI sequences that are obtained from BraTS datasets.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Notes

  1. 1.

    Multi-class classification can also be applied to this dataset for different grades of gliomas.

References

  1. Bahadure, N.B., Ray, A.K., Thethi, H.P.: Image analysis for MRI based brain tumor detection and feature extraction using biologically inspired BWT and SVM. Int. J. Biomed. Imaging 2017, 12 p. (2017). Article ID 9749108. https://doi.org/10.1155/2017/9749108

  2. Bahrami, K., Shi, F., Rekik, I., Gao, Y., Shen, D.: 7T-guided super-resolution of 3T MRI. Med. Phys. 44(5), 1661–1677 (2017)

    Article  Google Scholar 

  3. Bakas, S., et al.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4, 170117 (2017)

    Article  Google Scholar 

  4. 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)

  5. Benou, A., Veksler, R., Friedman, A., Raviv, T.R.: Ensemble of expert deep neural networks for spatio-temporal denoising of contrast-enhanced MRI sequences. Med. Image Anal. 42, 145–159 (2017)

    Article  Google Scholar 

  6. Bermudez, C., Plassard, A.J., Davis, L.T., Newton, A.T., Resnick, S.M., Landman, B.A.: Learning implicit brain MRI manifolds with deep learning. In: Medical Imaging 2018: Image Processing, vol. 10574, p. 105741L. International Society for Optics and Photonics (2018)

    Google Scholar 

  7. Chen, W., Liu, B., Peng, S., Sun, J., Qiao, X.: S3D-UNet: separable 3D U-Net for brain tumor segmentation. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 358–368. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_32

    Chapter  Google Scholar 

  8. Chen, Y., Shi, F., Christodoulou, A.G., Xie, Y., Zhou, Z., Li, D.: Efficient and accurate MRI super-resolution using a generative adversarial network and 3D multi-level densely connected network. In: Frangi, A.F., Schnabel, J.A., Davatzikos, C., Alberola-López, C., Fichtinger, G. (eds.) MICCAI 2018. LNCS, vol. 11070, pp. 91–99. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00928-1_11

    Chapter  Google Scholar 

  9. 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

    Chapter  Google Scholar 

  10. Falk, T., et al.: U-Net: deep learning for cell counting, detection, and morphometry. Nat. Methods 16(1), 67–70 (2019)

    Article  Google Scholar 

  11. Feng, Y., Pan, H., Meyer, C., Feng, X.: A self-adaptive network for multiple sclerosis lesion segmentation from multi-contrast MRI with various imaging protocols. arXiv preprint arXiv:1811.07491 (2018)

  12. Goodenberger, M.L., Jenkins, R.B.: Genetics of adult glioma. Cancer Genet. 205(12), 613–621 (2012)

    Article  Google Scholar 

  13. He, K., Zhang, X., Ren, S., Sun, J.: Deep residual learning for image recognition. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 770–778 (2016)

    Google Scholar 

  14. 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)

    Google Scholar 

  15. Işın, A., Direkoğlu, C., Şah, M.: Review of MRI-based brain tumor image segmentation using deep learning methods. Procedia Comput. Sci. 102, 317–324 (2016)

    Article  Google Scholar 

  16. Kauffmann, J., Müller, K., Montavon, G.: Towards explaining anomalies: a deep taylor decomposition of one-class models. Pattern Recognit. 101, 107198 (2020). https://doi.org/10.1016/j.patcog.2020.107198

    Article  Google Scholar 

  17. Khalid, N.E.A., Ibrahim, S., Haniff, P.: MRI brain abnormalities segmentation using k-nearest neighbors (K-NN). Int. J. Comput. Sci. Eng. 3(2), 980–990 (2011)

    Google Scholar 

  18. Kleihues, P., Soylemezoglu, F., Schäuble, B., Scheithauer, B.W., Burger, P.C.: Histopathology, classification, and grading of gliomas. Glia 15(3), 211–221 (1995)

    Article  Google Scholar 

  19. Kline, T.L., et al.: Performance of an artificial multi-observer deep neural network for fully automated segmentation of polycystic kidneys. J. Digit. Imaging 30(4), 442–448 (2017)

    Article  Google Scholar 

  20. Korfiatis, P., Kline, T.L., Lachance, D.H., Parney, I.F., Buckner, J.C., Erickson, B.J.: Residual deep convolutional neural network predicts MGMT methylation status. J. Digit. Imaging 30(5), 622–628 (2017)

    Article  Google Scholar 

  21. LeCun, Y., Bengio, Y., Hinton, G.: Deep learning. Nature 521(7553), 436 (2015)

    Article  Google Scholar 

  22. Li, H., Parikh, N.A., He, L.: A novel transfer learning approach to enhance deep neural network classification of brain functional connectomes. Front. Neurosci. 12, 491 (2018)

    Article  Google Scholar 

  23. Li, Y., Shen, L.: Skin lesion analysis towards melanoma detection using deep learning network. Sensors 18(2), 556 (2018)

    Article  Google Scholar 

  24. Litjens, G., et al.: A survey on deep learning in medical image analysis. Med. Image Anal. 42, 60–88 (2017)

    Article  Google Scholar 

  25. Makropoulos, A., Counsell, S.J., Rueckert, D.: A review on automatic fetal and neonatal brain MRI segmentation. NeuroImage 170, 231–248 (2018)

    Article  Google Scholar 

  26. Menze, B.H., et al.: The multimodal brain tumor image segmentation benchmark (brats). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2014)

    Article  Google Scholar 

  27. Montavon, G., Binder, A., Lapuschkin, S., Samek, W., Müller, K.-R.: Layer-wise relevance propagation: an overview. In: Samek, W., Montavon, G., Vedaldi, A., Hansen, L.K., Müller, K.-R. (eds.) Explainable AI: Interpreting, Explaining and Visualizing Deep Learning. LNCS (LNAI), vol. 11700, pp. 193–209. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-28954-6_10

    Chapter  Google Scholar 

  28. Narin, A., Kaya, C., Pamuk, Z.: Automatic detection of coronavirus disease (COVID-19) using X-ray images and deep convolutional neural networks. arXiv preprint arXiv:2003.10849 (2020)

  29. Oktay, O., et al.: Attention u-net: learning where to look for the pancreas. arXiv preprint arXiv:1804.03999 (2018)

  30. Pereira, S., Pinto, A., Alves, V., Silva, C.A.: Deep convolutional neural networks for the segmentation of gliomas in multi-sequence MRI. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Handels, H. (eds.) BrainLes 2015. LNCS, vol. 9556, pp. 131–143. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-30858-6_12

    Chapter  Google Scholar 

  31. 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

    Chapter  Google Scholar 

  32. Roser, M., Ritchie, H.: Cancer. Our World in Data (2020). https://ourworldindata.org/cancer

  33. Russakovsky, O., et al.: ImageNet large scale visual recognition challenge. Int. J. Comput. Vision (IJCV) 115(3), 211–252 (2015). https://doi.org/10.1007/s11263-015-0816-y

    Article  MathSciNet  Google Scholar 

  34. Schmidhuber, J.: Deep learning in neural networks: an overview. Neural Netw. 61, 85–117 (2015)

    Article  Google Scholar 

  35. Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014)

  36. Sun, J., Li, H., Xu, Z., et al.: Deep ADMM-net for compressive sensing MRI. In: Advances in Neural Information Processing Systems, pp. 10–18 (2016)

    Google Scholar 

  37. Szegedy, C., Vanhoucke, V., Ioffe, S., Shlens, J., Wojna, Z.: Rethinking the inception architecture for computer vision. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 2818–2826 (2016)

    Google Scholar 

  38. Tajbakhsh, N., et al.: On the necessity of fine-tuned convolutional neural networks for medical imaging. In: Lu, L., Zheng, Y., Carneiro, G., Yang, L. (eds.) Deep Learning and Convolutional Neural Networks for Medical Image Computing. ACVPR, pp. 181–193. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-42999-1_11

    Chapter  Google Scholar 

  39. Wang, S., et al.: Accelerating magnetic resonance imaging via deep learning. In: 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), pp. 514–517. IEEE (2016)

    Google Scholar 

  40. Zhou, X., et al.: Detection of pathological brain in MRI scanning based on wavelet-entropy and Naive Bayes classifier. In: Ortuño, F., Rojas, I. (eds.) IWBBIO 2015. LNCS, vol. 9043, pp. 201–209. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-16483-0_20

    Chapter  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Thierry Urruty .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Coupet, M. et al. (2020). An Empirical Study of Deep Neural Networks for Glioma Detection from MRI Sequences. In: Yang, H., Pasupa, K., Leung, A.CS., Kwok, J.T., Chan, J.H., King, I. (eds) Neural Information Processing. ICONIP 2020. Lecture Notes in Computer Science(), vol 12532. Springer, Cham. https://doi.org/10.1007/978-3-030-63830-6_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-63830-6_10

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-63829-0

  • Online ISBN: 978-3-030-63830-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics