Brain Tumor Segmentation and Radiomics Survival Prediction: Contribution to the BRATS 2017 Challenge

  • Fabian IsenseeEmail author
  • Philipp Kickingereder
  • Wolfgang Wick
  • Martin Bendszus
  • Klaus H. Maier-Hein
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10670)


Quantitative analysis of brain tumors is critical for clinical decision making. While manual segmentation is tedious, time consuming and subjective, this task is at the same time very challenging to solve for automatic segmentation methods. In this paper we present our most recent effort on developing a robust segmentation algorithm in the form of a convolutional neural network. Our network architecture was inspired by the popular U-Net and has been carefully modified to maximize brain tumor segmentation performance. We use a dice loss function to cope with class imbalances and use extensive data augmentation to successfully prevent overfitting. Our method beats the current state of the art on BraTS 2015, is one of the leading methods on the BraTS 2017 validation set (dice scores of 0.896, 0.797 and 0.732 for whole tumor, tumor core and enhancing tumor, respectively) and achieves very good Dice scores on the test set (0.858 for whole, 0.775 for core and 0.647 for enhancing tumor). We furthermore take part in the survival prediction subchallenge by training an ensemble of a random forest regressor and multilayer perceptrons on shape features describing the tumor subregions. Our approach achieves 52.6% accuracy, a Spearman correlation coefficient of 0.496 and a mean square error of 209607 on the test set.


CNN Brain tumor Glioblastoma Deep learning 


  1. 1.
    Menze, B.H., Jakab, A., Bauer, S., Kalpathy-Cramer, J., Farahani, K., Kirby, J., Burren, Y., Porz, N., Slotboom, J., Wiest, R., et al.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2015)CrossRefGoogle Scholar
  2. 2.
    Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J., Freymann, J., Farahani, K., Davatzikos, C.: Advancing the cancer genome Atlas Glioma MRI collections with expert segmentation labels and radiomic features. Nature Scientific Data (2017, in Press)Google Scholar
  3. 3.
    Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J., Freymann, J., Farahani, K., Davatzikos, C.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-GBM collection. In: TCIA (2017)Google Scholar
  4. 4.
    Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J., Freymann, J., Farahani, K., Davatzikos, C.: Segmentation labels and radiomic features for the pre-operative scans of the TCGA-LGG collection. In: TCIA (2017)Google Scholar
  5. 5.
    Havaei, M., Davy, A., Warde-Farley, D., Biard, A., Courville, A., Bengio, Y., Pal, C., Jodoin, P.-M., Larochelle, H.: Brain tumor segmentation with deep neural networks. Med. Image Anal. 35, 18–31 (2017)CrossRefGoogle Scholar
  6. 6.
    Pereira, S., Pinto, A., Alves, V., Silva, C.A.: Brain tumor segmentation using convolutional neural networks in MRI images. IEEE Trans. Med. Imaging 35(5), 1240–1251 (2016)CrossRefGoogle Scholar
  7. 7.
    Kamnitsas, K., Ledig, C., Newcombe, V.F., Simpson, J.P., Kane, A.D., Menon, D.K., Rueckert, D., Glocker, B.: Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation. Med. Image Anal. 36, 61–78 (2017)CrossRefGoogle Scholar
  8. 8.
    Kamnitsas, K., Ferrante, E., Parisot, S., Ledig, C., Nori, A.V., Criminisi, A., Rueckert, D., Glocker, B.: DeepMedic for brain tumor segmentation. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Handels, H. (eds.) BrainLes 2015. LNCS, vol. 9556. Springer, Cham (2016). Google Scholar
  9. 9.
    Kayalibay, B., Jensen, G., van der Smagt, P.: CNN-based segmentation of medical imaging data. arXiv preprint arXiv:1701.03056 (2017)
  10. 10.
    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). CrossRefGoogle Scholar
  11. 11.
    Milletari, F., Navab, N., Ahmadi, S.-A.: V-Net: fully convolutional neural networks for volumetric medical image segmentation. In: International Conference on 3D Vision, pp. 565–571. IEEE (2016)Google Scholar
  12. 12.
    Macyszyn, L., Akbari, H., Pisapia, J.M., Da, X., Attiah, M., Pigrish, V., Bi, Y., Pal, S., Davuluri, R.V., Roccograndi, L., et al.: Imaging patterns predict patient survival and molecular subtype in glioblastoma via machine learning techniques. Neuro-oncology 18(3), 417–425 (2015)CrossRefGoogle Scholar
  13. 13.
    He, K., Zhang, X., Ren, S., Sun, J.: Identity mappings in deep residual networks. In: Leibe, B., Matas, J., Sebe, N., Welling, M. (eds.) ECCV 2016. LNCS, vol. 9908, pp. 630–645. Springer, Cham (2016). CrossRefGoogle Scholar
  14. 14.
    Ulyanov, D., Vedaldi, A., Lempitsky, V.: Instance normalization: the missing ingredient for fast stylization. arXiv preprint arXiv:1607.08022 (2016)
  15. 15.
    Kingma, D., Ba, J.: Adam: a method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014)
  16. 16.
    van Griethuysen, J.J.M., Fedorov, A., Parmar, C., Hosny, A., Aucoin, N., Narayan, V., Beets-Tan, R.G.H., Fillion-Robin, J.-C., Pieper, S., Aerts, H.J.W.L.: Computational radiomics system to decode the radiographic phenotype. Cancer Research (2017, accepted)Google Scholar
  17. 17.
    Kohavi, R., John, G.H.: Wrappers for feature subset selection. Artif. Intell. 97(1–2), 273–324 (1997)CrossRefzbMATHGoogle Scholar
  18. 18.
    Brown, G.: A new perspective for information theoretic feature selection. In: Artificial Intelligence and Statistics, pp. 49–56 (2009)Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Fabian Isensee
    • 1
    Email author
  • Philipp Kickingereder
    • 2
  • Wolfgang Wick
    • 3
  • Martin Bendszus
    • 2
  • Klaus H. Maier-Hein
    • 1
  1. 1.Division of Medical Image ComputingGerman Cancer Research Center (DKFZ)HeidelbergGermany
  2. 2.Department of NeuroradiologyHeidelberg University HospitalHeidelbergGermany
  3. 3.Neurology ClinicHeidelberg University HospitalHeidelbergGermany

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