Nothing Special   »   [go: up one dir, main page]

Skip to main content

Brain White Matter Lesion Segmentation with 2D/3D CNN

  • Conference paper
  • First Online:
Natural and Artificial Computation for Biomedicine and Neuroscience (IWINAC 2017)

Abstract

Automated detection of white matter hyperintensities (WHM) may have a broad clinical use, because WHM appear in several brain diseases. Deep learning architectures have been recently very successful for the segmentation of brain lesions, such as ictus or tumour lesions. We propose a Convolutional Neural Network composed of four parallel data paths whose input is a mixture of 2D/3D windows extracted from multimodal magnetic resonance imaging of the brain. The architecture is lighter than others proposed in the literature for lesion detection so its training is faster. We carry out computational experiments on a dataset of multimodal imaging from 18 subjects, achieving competitive results with state of the art approaches.

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

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
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

Institutional subscriptions

Similar content being viewed by others

References

  1. Admiraal-Behloul, F., van den Heuvel, D.M.J., Olofsen, H., van Osch, M.J.P., van der Grond, J., van Buchem, M.A., Reiber, J.H.C.: Fully automatic segmentation of white matter hyperintensities in MR images of the elderly. NeuroImage 28(3), 607–617 (2005)

    Article  Google Scholar 

  2. Brosch, T., Yoo, Y., Tang, L.Y.W., Li, D.K.B., Traboulsee, A., Tam, R.: Deep convolutional encoder networks for multiple sclerosis lesion segmentation. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9351, pp. 3–11. Springer, Cham (2015). doi:10.1007/978-3-319-24574-4_1

    Chapter  Google Scholar 

  3. Ciresan, D., Giusti, A., Gambardella, L.M., Schmidhuber, J.: Deep neural networks segment neuronal membranes in electron microscopy images. In: Advances in Neural Information Processing Systems, pp. 2843–2851 (2012)

    Google Scholar 

  4. de Brébisson, A., Montana, G.: Deep neural networks for anatomical brain segmentation. In: 2015 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW), pp. 20–28, June 2015

    Google Scholar 

  5. Debette, S., Markus, H.S.: The clinical importance of white matter hyperintensities on brain magnetic resonance imaging: systematic review and meta-analysis. BMJ 341, c3666 (2010)

    Article  Google Scholar 

  6. Erihov, M., Alpert, S., Kisilev, P., Hashoul, S.: A Cross saliency approach to asymmetry-based tumor detection. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9351, pp. 636–643. Springer, Cham (2015). doi:10.1007/978-3-319-24574-4_76

    Chapter  Google Scholar 

  7. Gao, X.W., Hui, R., Tian, Z.: Classification of CT brain images based on deep learning networks. Comput. Methods Programs Biomed. 138, 49–56 (2017)

    Article  Google Scholar 

  8. Geremia, E., Clatz, O., Menze, B.H., Konukoglu, E., Criminisi, A., Ayache, N.: Spatial decision forests for MS lesion segmentation in multi-channel magnetic resonance images. NeuroImage 57(2), 378–390 (2011)

    Article  Google Scholar 

  9. Schulz, U.G., Grueter, B.E.: Age-related cerebral white matter disease (Leukoaraiosis): a review. Postgrad. Med. J. 88, 79–87 (2012)

    Article  Google Scholar 

  10. 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)

    Article  Google Scholar 

  11. Iorio, M., Spalletta, G., Chiapponi, C., Luccichenti, G., Cacciari, C., Orfei, M.D., Caltagirone, C., Piras, F.: White matter hyperintensities segmentation: a new semi-automated method. Front. Aging Neurosci. 5, 76 (2013)

    Article  Google Scholar 

  12. Kamnitsas, K., Ledig, C., Newcombe, V.F.J., 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)

    Article  Google Scholar 

  13. Lecun, Y., Bottou, L., Bengio, Y., Haffner, P.: Gradient-based learning applied to document recognition. Proc. IEEE 86(11), 2278–2324 (1998)

    Article  Google Scholar 

  14. LeCun, Y., Bengio, Y., Hinton, G.: Deep learning. Nature 521(7553), 436–444 (2015)

    Article  Google Scholar 

  15. Murray, A.D., Staff, R.T., Shenkin, S.D., Deary, I.J., Starr, J.M., Whalley, L.J.: Brain white matter hyperintensities: relative importance of vascular risk factors in nondemented elderly people. Radiology 237, 251–257 (2005)

    Article  Google Scholar 

  16. Payne, M.E., et al.: Development of a semi-automated method for quantification of MRI gray and white matter lesions in geriatric subjects. Psychiatry Res.: Neuroimaging 115(1), 63–77 (2002)

    Article  Google Scholar 

  17. Pelletier, A., Periot, O., Dilharreguy, B., Hiba, B., Bordessoules, M., Chanraud, S., Pérés, K., Amieva, H., Dartigues, J., Allard, M., Catheline, G.: Age-related modifications of diffusion tensor imaging parameters and white matter hyperintensities as inter-dependent processes. Front. Aging Neurosci. 7(255) (2016)

    Google Scholar 

  18. 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). doi:10.1007/978-3-319-30858-6_12

    Chapter  Google Scholar 

  19. Price, C.C., Mitchell, S.M., Brumback, B., Tanner, J.J., Schmalfuss, I., Lamar, M., Giovannetti, T., Heilman, K.M., Libon, D.J.: MRI-Leukoaraiosis thresholds and the phenotypic expression of dementia. Neurology 79(8), 734–740 (2012)

    Article  Google Scholar 

  20. Schwarz, C., Fletcher, E., DeCarli, C., Carmichael, O.: Fully-automated white matter hyperintensity detection with anatomical prior knowledge and without FLAIR. In: Prince, J.L., Pham, D.L., Myers, K.J. (eds.) IPMI 2009. LNCS, vol. 5636, pp. 239–251. Springer, Heidelberg (2009). doi:10.1007/978-3-642-02498-6_20

    Chapter  Google Scholar 

  21. Tuladhar, A.M., van Dijk, E., Zwiers, M.P., van Norden, A.G.W., de Laat, K.F., Shumskaya, E., Norris, D.G., de Leeuw, F.-E.: Structural network connectivity and cognition in cerebral small vessel disease. Hum. Brain Mapp. 37(1), 300–310 (2016)

    Article  Google Scholar 

  22. Tustison, N., Wintermark, M., Durst, C., Avants, B.: Miccai society, ants and árboles. In: MICCAI BraTS Workshop, Nagoya (2013)

    Google Scholar 

  23. Uchiyama, Y., Kunieda, T., Hara, T., Fujita, H., Ando, H., Yamakawa, H., Asano, T., Kato, H., Iwama, T., Kanematsu, M., Hoshi, H.: Automatic segmentation of different-sized Leukoaraiosis regions in brain MR images. In: Proceedings of SPIE, vol. 6915, pp. 69151S–69151S-8 (2008)

    Google Scholar 

  24. Urban, G., Bendszus, M., Hamprecht, F., Kleesiek, J.: Multi-modal brain tumor segmentation using deep convolutional neural networks. In: MICCAI BraTS (Brain Tumor Segmentation) Challenge: Proceedings, Winning Contribution, pp. 31–35 (2014)

    Google Scholar 

  25. Yoshita, M., Fletcher, E., Harvey, D., Ortega, M., Martinez, O., Mungas, D.M., Reed, B.R., DeCarli, C.S.: Extent and distribution of white matter hyperintensities in normal aging, MCI, and AD. Neurology 67(12), 2192–2198 (2006)

    Article  Google Scholar 

  26. Zikic, D., Ioannou, Y., Brown, M., Criminisi, A.: Segmentation of brain tumor tissues with convolutional neural networks. In: Proceedings MICCAI-BRATS, pp. 36–39 (2014)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to M. Graña .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this paper

Cite this paper

López-Zorrilla, A. et al. (2017). Brain White Matter Lesion Segmentation with 2D/3D CNN. In: Ferrández Vicente, J., Álvarez-Sánchez, J., de la Paz López, F., Toledo Moreo, J., Adeli, H. (eds) Natural and Artificial Computation for Biomedicine and Neuroscience. IWINAC 2017. Lecture Notes in Computer Science(), vol 10337. Springer, Cham. https://doi.org/10.1007/978-3-319-59740-9_39

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-59740-9_39

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-59739-3

  • Online ISBN: 978-3-319-59740-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics