Abstract
This Grand Challenge at MICCAI 2017 aims to directly compare methods for the automatic segmentation of White Matter Hyperintensities (WMH) of presumed vascular origin. Our method automatically segment WMH by using texture-based classification of pixels within the brain white matter. It uses no a priori information about the WMH size, contrast or location. The main goal is to compute the probability of each pixel being normal or WMH tissue, by generating a probability map. Based on this probability map, we can automatically segment the WMHs.
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References
Appenzeller, S., Vasconcelos Faria, A., Li, L.M., Costallat, L.T., Cendes, F.: Quantitativemagnetic resonance imaging analyses and clinical significance of hyperintense white matter lesions in systemic lupus erythematosus patients. Ann. Neurol. 64(6), 635–643 (2008)
Bento, M., Rittner, L., Lotufo, R.: Texture descriptors and pattern recognition classifiers based analysis of white matter hyperintensity in MR images. In: Proceedings of Workshop of Theses and Dissertations in SIBGRAPI 2013 (XXVI Conference on Graphics, Patterns and Images) (2013)
Bento, M., Sym, Y., Frayne, R., Lotufo, R., Rittner, L.: Probabilistic segmentation of brain white matter lesions using texture-based classification. In: Karray, F., Campilho, A., Cheriet, F. (eds.) ICIAR 2017. LNCS, vol. 10317, pp. 71–78. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-59876-5_9
Calabrese, M., Rocca, M., Atzori, M., Mattisi, I., Bernardi, V., Favaretto, A., Barachino, L., Romualdi, C., Rinaldi, L., Perini, P., Gallo, P., Filippi, M.: Cortical lesions in primary progressive multiple sclerosis: a 2-year longitudinal MR study. Neurology 72(15), 1330–1336 (2009)
Chen, L., Bentley, P., Rueckert, D.: A novel framework for sub-acute stroke lesion segmentation based on random forest. In: Proceedings of Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: First International Workshop, Brainles 2015, Held in Conjunction with MICCAI 2015 (2015)
Despotovic, I., Goossens, B., Philips, W.: MRI segmentation of the human brain: challenges, methods, and applications. Comput. Math. Methods Med. 2015(1), 1–23 (2015)
Feng, C., Zhao, D., Huang, M.: Segmentation of Ischemic stroke lesions in multi-spectral MR images using weighting suppressed FCM and three phase level set. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Handels, H. (eds.) BrainLes 2015. LNCS, vol. 9556, pp. 233–245. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-30858-6_20
Griffanti, L., Zamboni, G., Khan, A., Li, L., Bonifacio, G., Sundaresan, V., Schulz, U., Kuker, W., Battaglini, M., Rothwell, P., Jenkinson, M.: BIANCA (Brain Intensity Abnormality Classification Algorithm): a new tool for automated segmentation of white matter hyperintensities. NeuroImage 141, 191–205 (2016)
He, D.C., Wang, L.: Texture unit, texture spectrum, and texture analysis. IEEE Trans. Geosci. Remote Sens. 28(1), 509–512 (1990)
Ithapu, V., Singh, V., Lindner, C., Austin, B., Hinrichs, C., Carlsson, C., Bendlin, B., Johnson, S.: Extracting and summarizing white matter hyperintensities using supervised segmentation methods in Alzheimer’s disease risk and aging studies. Hum. Brain Mapping 35(1), 4219–4235 (2014)
Jones, E., Oliphant, T., Peterson, P., et al.: SciPy: open source scientific tools for Python (2001). http://www.scipy.org/
Kamnitsas, K., Chen, L., Ledig, C., Rueckert, D., Glocker, B.: Multi-scale 3D convolutional neural networks for lesion segmentation in brain MRI. In: Proceedings of Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: First International Workshop, Brainles 2015, Held in Conjunction with MICCAI 2015 (2015)
Kashif, M., Raza, S., Sirinukunwattana, K., Arif, M., Rajpoot, N.: Handcrafted features with convolutional neural networks for detection of tumor cells in histology images. In: Proceedings of IEEE 13th International Symposium on Biomedical Imaging (2016)
Kloppenborg, R., Nederkoorn, P., Geerlings, M., Berg, E.: Presence and progression of white matter hyperintensities and cognition: a meta-analysis. Neurology 82(1), 2127–2138 (2014)
Lao, Z., Shen, D., Liu, D., Jawad, A.F., Melhem, E.R., Launer, L.J., Bryan, R.N., Davatzikos, C.: Computer-assisted segmentation of white matter lesions in 3D MR images, using support vector machine. Acad. Radiol. 15(3), 300–313 (2008)
Lapa, A., Bento, M., Rittner, L., Ruocco, H., Castellano, G., Damasceno, B., Costallat, L., Lotufo, R., Cendes, F., Appenzeller, S.: Support vector machines classification of texture parameters of white matter lesions in childhood-onset systemic lupus erythematosus. Possible mechanism to distinguish between demyelination and ischemia. Ann. Rheum. Dis. 71(269) (2013)
Leite, M., Gobbi, D., Salluzi, M., Frayne, R., Lotufo, R., Rittner, L.: 3D texture-based classification applied on brain white matter lesions on MR images. In: Proceedings Volume 9785: Medical Imaging 2016: Computer-Aided Diagnosis SPIE (2016)
Leite, M., Lapa, A., Appenzeller, S., Lotufo, R., Rittner, L.: A new approach for longitudinal study of white matter lesion based on texture variation. In: Proceedings of XXV Congresso Brasileiro de Engenharia Biomédica (2016)
Leite, M., Rittner, L., Appenzeller, S., Ruocco, H., Lotufo, R.: Etiology-based classification of brain white matter hyperintensity on magnetic resonance imaging. J. Med. Imaging 2(1), 014002-1–014002-10 (2015)
Loizou, C., Petroudi, S., Seimenis, I., Seimenis, I., Pantziaris, M.: Pattichis: quantitative texture analysis of brain white matter lesions derived from T2-weighted MR images in MS patients with clinically isolated syndrome. Neuroradiology 42(2), 99–114 (2015)
Loizou, C., Seimenis, I., Seimenis, I., Pantziaris, M., Kasparis, T., Kyriacou, E., Pattichis, C.: Texture image analysis of normal appearing white matter areas in clinically isolated syndrome that evolved in demyelinating lesions in subsequent MRI scans: multiple sclerosis disease evolution. In: Proceedings of the 10th IEEE International Conference on Information Technology and Applications in Biomedicine (2010)
Merkel, D.: Docker: lightweight Linux containers for consistent development and deployment. Linux J. 2014(239) (2014). Article No. 2
Mortazavi, D., Kouzani, A., Soltanian, H.: Segmentation of multiple sclerosis lesions in MR images: a review. Neuroradiology 54(4), 299–320 (2012)
Nourbakhsh, B., Nunan-Saah, J., Maghzi, A., Julian, L., Spain, R., Jin, C., Lazar, A., Pelletier, D., Waubant, E.: Longitudinal associations between MRI and cognitive changes in very early MS. Multiple Sclerosis Relat. Disord. 5(1), 47–52 (2016)
Oppedal, K., Eftestol, T., Engan, K., Beyer, M., Aarsland, D.: Classifying dementia using local binary patterns from different regions in magnetic resonance images. Int. J. Biomed. Imaging 2015, 1–14 (2015)
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V., Vanderplas, J., Passos, A., Cournapeau, D., Brucher, M., Perrot, M., Duchesnay, E.: Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12(1), 2825–2830 (2011)
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
Roura, E., Oliver, A., Cabezas, M., Valverde, S., Pareto, D., Vilanova, J., Ramió-Torrentà, L., Rovira, A., Lladó, X.: A toolbox for multiple sclerosis lesion segmentation. Neuroradiology 57(10), 1031–1043 (2015)
Roura, E., Sarbu, N., Oliver, A., Valverde, S., González-Villà, S., Cervera, R., Bargalló, N., Lladó, X.: Automated detection of lupus white matter lesions in MRI. Front. Neuroinformatics 10(33), 1–11 (2016)
Salembier, P., Oliveras, A., Garrido, L.: Antiextensive connected operators for image and sequence processing. IEEE Trans. Image Process. 7(4), 555–570 (1998)
Samet, H., Tamminen, M.: Efficient component labeling of images of arbitrary dimension represented by linear bintrees. IEEE Trans. Pattern Anal. Mach. Intell. 10(4), 579 (1988)
Stankiewicz, J., Glanz, B., Healy, B., Arora, A., Neema, M., Benedict, R., Guss, Z., Tauhid, S., Buckle, G., Houtchens, M., Khoury, S., Weiner, H., Guttmann, C., Bakshi, R.: Brain MRI lesion load at 1.5T and 3T vs. clinical status in multiple sclerosis. J. Neuroimaging 21(2), 1–15 (2011)
Steenwijk, M., Pouwels, P., Daams, M., Dalen, J., Caan, M., Richard, E., Barkhof, F., Vrenken, H.: Accurate white matter lesion segmentation by k nearest neighbor classification with tissue type priors (kNN-TTPs). NeuroImage Clin. 3, 462–469 (2013)
Sudre, C., Cardoso, M., Ourselin, S.: Longitudinal segmentation of age-related white matter hyperintensities. Med. Image Anal. 38, 50–64 (2017)
Taha, A., Hanbury, A.: Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool. BMC Med. Imaging 15(29), 1–29 (2015)
Vernooij, M., Ikram, M., Tanghe, H., Vincent, A., Hofman, A., Krestin, G., Niessen, W., Breteler, M., van der Lugt, A.: Incidental findings on brain MRI in the general population. New England J. Med. 357(18), 1821–1828 (2007)
Walt, S., Colbert, S., Varoquaux, G.: The NumPy array: a structure for efficient numerical computation. Comput. Sci. Eng. 13, 22–30 (2011)
van der Walt, S., Schönberger, J.L., Nunez-Iglesias, J., Boulogne, F., Warner, J.D., Yager, N., Gouillart, E., Yu, T.: The scikit-image contributors: Scikit-image: image processing in Python. Peer J. Bioinform. Software Tools Collect. 2, e453 (2014)
Zhang, Y.: MRI texture analysis in multiple sclerosis. Int. J. Biomed. Imaging 2012, 1–7 (2012). Article ID 762804
Acknowledgments
The authors would like to thank Hotchkiss Brain Institute; CAPES process PVE 88881.062158/2014-01; FAPESP processes 2012/21826-1 CEPID2013/07559-3 for providing financial support.
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Bento, M., de Souza, R., Lotufo, R., Frayne, R., Rittner, L. (2018). WMH Segmentation Challenge: A Texture-Based Classification Approach. In: Crimi, A., Bakas, S., Kuijf, H., Menze, B., Reyes, M. (eds) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2017. Lecture Notes in Computer Science(), vol 10670. Springer, Cham. https://doi.org/10.1007/978-3-319-75238-9_41
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