Abstract
White matter tract segmentation based on diffusion magnetic resonance imaging (dMRI) plays an important role in brain analysis. Deep learning based methods of white matter tract segmentation have been proposed to improve the segmentation accuracy. However, manual delineations of white matter tracts for network training are especially difficult to obtain. Therefore, in this paper, we explore how to improve the performance of deep learning based white matter tract segmentation when the number of manual tract delineations is limited. Specifically, we propose to exploit the abundant unannotated data using a self-supervised learning approach, where knowledge about image context can be learned in a well designed pretext task that does not require manual annotations. The knowledge can then be transferred to the white matter tract segmentation task, so that when manual tract delineations for training are scarce, the performance of the network can be improved. To allow the image context knowledge to be relevant to white matter tracts, the pretext task in this work is designed to predict the density map of fiber streamlines, where training data can be obtained using tractography without manual efforts. The model pretrained for the pretext task is then fine-tuned by the small number of tract annotations for the target segmentation task. In addition, we explore the possibility of combining self-supervised learning with a complementary pseudo-labeling strategy of using unannotated data. We validated the proposed approach using dMRI scans from the Human Connectome Project dataset, where the benefit of the proposed method is shown when tract annotations are scarce.
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Notes
- 1.
The TractSeg code is available at https://github.com/MIC-DKFZ/TractSeg/.
- 2.
The annotations are available at https://doi.org/10.5281/zenodo.1088277.
- 3.
For the meaning of the abbreviations for tract names, refer to [18].
References
Bai, W., et al.: Semi-supervised learning for network-based cardiac MR image segmentation. In: Descoteaux, M., Maier-Hein, L., Franz, A., Jannin, P., Collins, D.L., Duchesne, S. (eds.) MICCAI 2017. LNCS, vol. 10434, pp. 253–260. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-66185-8_29
Basser, P.J., Pajevic, S., Pierpaoli, C., Duda, J., Aldroubi, A.: In vivo fiber tractography using DT-MRI data. Magn. Reson. Med. 44(4), 625–632 (2000)
Bazin, P.L., et al.: Direct segmentation of the major white matter tracts in diffusion tensor images. NeuroImage 58(2), 458–468 (2011)
Doersch, C., Gupta, A., Efros, A.A.: Unsupervised visual representation learning by context prediction. In: Proceedings of the IEEE International Conference on Computer Vision, pp. 1422–1430 (2015)
Garyfallidis, E., et al.: Dipy, a library for the analysis of diffusion MRI data. Front. Neuroinform. 8(8), 1–17 (2014)
Glasser, M.F., et al.: The minimal preprocessing pipelines for the human connectome project. NeuroImage 80, 105–124 (2013)
Jeurissen, B., Tournier, J.D., Dhollander, T., Connelly, A., Sijbers, J.: Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage 103, 411–426 (2014)
Kingma, D.P., Ba, J.: Adam: a method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014)
Nair, V., Hinton, G.E.: Rectified linear units improve restricted Boltzmann machines. In: Proceedings of the 27th International Conference on Machine Learning, pp. 807–814 (2010)
Paszke, A., et al.: PyTorch: an imperative style, high-performance deep learning library. In: Advances in Neural Information Processing Systems, pp. 8024–8035 (2019)
Pathak, D., Krahenbuhl, P., Donahue, J., Darrell, T., Efros, A.A.: Context encoders: feature learning by inpainting. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 2536–2544 (2016)
Ratnarajah, N., Qiu, A.: Multi-label segmentation of white matter structures: application to neonatal brains. NeuroImage 102, 913–922 (2014)
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
Srivastava, N., Hinton, G., Krizhevsky, A., Sutskever, I., Salakhutdinov, R.: Dropout: a simple way to prevent neural networks from overfitting. J. Mach. Learn. Res. 15(1), 1929–1958 (2014)
Taha, A.A., Hanbury, A.: Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool. BMC Med. Imaging 15(1), 29 (2015)
Tournier, J.D., Calamante, F., Connelly, A.: Robust determination of the fibre orientation distribution in diffusion MRI: non-negativity constrained super-resolved spherical deconvolution. NeuroImage 35(4), 1459–1472 (2007)
Van Essen, D.C., Smith, S.M., Barch, D.M., Behrens, T.E., Yacoub, E., Ugurbil, K.: Wu-Minn HCP Consortium: the WU-Minn human connectome project: an overview. NeuroImage 80, 62–79 (2013)
Wasserthal, J., Neher, P., Maier-Hein, K.H.: TractSeg - fast and accurate white matter tract segmentation. NeuroImage 183, 239–253 (2018)
Ye, C., Yang, Z., Ying, S.H., Prince, J.L.: Segmentation of the cerebellar peduncles using a random forest classifier and a multi-object geometric deformable model: application to spinocerebellar ataxia type 6. Neuroinformatics 13(3), 367–381 (2015)
Zhang, F., Hoffmann, N., Karayumak, S.C., Rathi, Y., Golby, A.J., O’Donnell, L.J.: Deep white matter analysis: fast, consistent tractography segmentation across populations and dMRI acquisitions. In: Shen, D., et al. (eds.) MICCAI 2019. LNCS, vol. 11766, pp. 599–608. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32248-9_67
Acknowledgements
This work is supported by Beijing Natural Science Foundation (L192058 & 7192108) and Beijing Institute of Technology Research Fund Program for Young Scholars. The HCP dataset was provided by the Human Connectome Project, WU-Minn Consortium and the McDonnell Center for Systems Neuroscience at Washington University.
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Lu, Q., Li, Y., Ye, C. (2020). White Matter Tract Segmentation with Self-supervised Learning. In: Martel, A.L., et al. Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science(), vol 12267. Springer, Cham. https://doi.org/10.1007/978-3-030-59728-3_27
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