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An Integrative Analysis of Image Segmentation and Survival of Brain Tumour Patients

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Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries (BrainLes 2019)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 11992))

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Abstract

Our contribution to the BraTS 2019 challenge consisted of a deep learning based approach for segmentation of brain tumours from MR images using cross validation ensembles of 2D-UNet models. Furthermore, different approaches for the prediction of patient survival time using clinical as well as imaging features were investigated. A simple linear regression model using patient age and tumour volumes outperformed more elaborate approaches like convolutional neural networks or radiomics-based analysis with an accuracy of 0.55 on the validation cohort and 0.51 on the test cohort.

S. Starke and C. Eckert—Shared first authorship.

S. Löck and S. Leger—Shared senior authorship.

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References

  1. 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 

  2. 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 

  3. Bakas, S., Reyes, M., Jakab, A., Bauer, S., Rempfler, M., Crimi, et al.: Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge. arXiv e-prints arXiv:1811.02629, November 2018

  4. 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

  5. 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

  6. Tustison, N.J., et al.: N4ITK: improved N3 bias correction. IEEE Trans. Med. Imaging 29(6), 1310 (2010)

    Article  Google Scholar 

  7. Manjón, J.V., Coupé, P., Martí-Bonmatí, L., Collins, D.L., Robles, M.: Adaptive non-local means denoising of MR images with spatially varying noise levels. J. Magn. Reson. Imaging 31(1), 192–203 (2010)

    Article  Google Scholar 

  8. 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 

  9. Aerts, H.J., et al.: Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nat. Commun. 5, 4006 (2014)

    Article  Google Scholar 

  10. Vallières, M., Freeman, C.R., Skamene, S.R., El Naqa, I.: A radiomics model from joint FDG-PET and MRI texture features for the prediction of lung metastases in soft-tissue sarcomas of the extremities. Phys. Med. Biol. 60(14), 5471 (2015)

    Article  Google Scholar 

  11. Coroller, T.P., et al.: CT-based radiomic signature predicts distant metastasis in lung adenocarcinoma. Radiother. Oncol. 114(3), 345–350 (2015)

    Article  Google Scholar 

  12. Haralick, R.M., Shanmugam, K., Dinstein, I., et al.: Textural features for image classification. IEEE Trans. Syst. Man Cybern. 3(6), 610–621 (1973)

    Article  Google Scholar 

  13. Galloway, M.M.: Texture analysis using grey level run lengths. NASA STI/Recon Technical report N 75 (1974)

    Google Scholar 

  14. Dasarathy, B.V., Holder, E.B.: Image characterizations based on joint gray level-run length distributions. Pattern Recognit. Lett. 12(8), 497–502 (1991)

    Article  Google Scholar 

  15. Amadasun, M., King, R.: Textural features corresponding to textural properties. IEEE Trans. Syst. Man Cybern. 19(5), 1264–1274 (1989)

    Article  Google Scholar 

  16. Thibault, G., et al.: Texture indexes and gray level size zone matrix application to cell nuclei classification. Pattern Recognit. Inf. Process., 140–145 (2009)

    Google Scholar 

  17. Thibault, G., Angulo, J., Meyer, F.: Advanced statistical matrices for texture characterization: application to cell classification. IEEE Trans. Biomed. Eng. 61(3), 630–637 (2014)

    Article  Google Scholar 

  18. Sun, C., Wee, W.G.: Neighboring gray level dependence matrix for texture classification. Comput. Vis. Graph. Image Process. 23(3), 341–352 (1983)

    Article  Google Scholar 

  19. Gómez, W., Pereira, W.C.A., Infantosi, A.F.C.: Analysis of co-occurrence texture statistics as a function of gray-level quantization for classifying breast ultrasound. IEEE Trans. Med. Imaging 31(10), 1889–1899 (2012)

    Article  Google Scholar 

  20. Clausi, D.A.: An analysis of co-occurrence texture statistics as a function of grey level quantization. Can. J. Remote Sens. 28(1), 45–62 (2002)

    Article  Google Scholar 

  21. Zwanenburg, A., Leger, S., Vallières, M., Löck, S.: Image biomarker standardisation initiative. arXiv preprint arXiv:1612.07003 (2016)

  22. Parmar, C., Grossmann, P., Bussink, J., Lambin, P., Aerts, H.J.: Machine learning methods for quantitative radiomic biomarkers. Sci. Rep. 5, 13087 (2015)

    Article  Google Scholar 

  23. Leger, S., et al.: A comparative study of machine learning methods for time-to-event survival data for radiomics risk modelling. Sci. Rep. 7(1), 13206 (2017)

    Article  MathSciNet  Google Scholar 

  24. Spearman, C.: Correlation calculated from faulty data. Br. J. Psychol. 1904-1920 3(3), 271–295 (1910)

    Article  Google Scholar 

  25. Battiti, R.: Using mutual information for selecting features in supervised neural net learning. IEEE Trans. Neural Netw. 5(4), 537–550 (1994)

    Article  Google Scholar 

  26. Peng, H., Long, F., Ding, C.: Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans. Pattern Anal. Mach. Intell. 27(8), 1226–1238 (2005)

    Article  Google Scholar 

  27. Ishwaran, H., Kogalur, U.B., Blackstone, E.H., Lauer, M.S.: Random survival forests. Ann. Appl. Stat. 2(3), 841–860 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  28. Hothorn, T., Bühlmann, P., Kneib, T., Schmid, M., Hofner, B.: Model-based boosting 2.0. J. Mach. Learn. Res. 11(Aug), 2109–2113 (2010)

    MathSciNet  MATH  Google Scholar 

  29. Parmar, C., et al.: Radiomic feature clusters and prognostic signatures specific for lung and head & neck cancer. Sci. Rep. 5, 11044 (2015)

    Article  Google Scholar 

  30. Dietterich, T.G.: Ensemble methods in machine learning. In: Kittler, J., Roli, F. (eds.) MCS 2000. LNCS, vol. 1857, pp. 1–15. Springer, Heidelberg (2000). https://doi.org/10.1007/3-540-45014-9_1

    Chapter  Google Scholar 

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Acknowledgment

The author SLe is supported by the Federal Ministry of Education and Research (BMBF-13GW0211D).

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Correspondence to Sebastian Starke .

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Starke, S., Eckert, C., Zwanenburg, A., Speidel, S., Löck, S., Leger, S. (2020). An Integrative Analysis of Image Segmentation and Survival of Brain Tumour Patients. In: Crimi, A., Bakas, S. (eds) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2019. Lecture Notes in Computer Science(), vol 11992. Springer, Cham. https://doi.org/10.1007/978-3-030-46640-4_35

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  • DOI: https://doi.org/10.1007/978-3-030-46640-4_35

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