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2017 | OriginalPaper | Buchkapitel

Automatic Brain Tumor Detection and Segmentation Using U-Net Based Fully Convolutional Networks

verfasst von : Hao Dong, Guang Yang, Fangde Liu, Yuanhan Mo, Yike Guo

Erschienen in: Medical Image Understanding and Analysis

Verlag: Springer International Publishing

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Abstract

A major challenge in brain tumor treatment planning and quantitative evaluation is determination of the tumor extent. The noninvasive magnetic resonance imaging (MRI) technique has emerged as a front-line diagnostic tool for brain tumors without ionizing radiation. Manual segmentation of brain tumor extent from 3D MRI volumes is a very time-consuming task and the performance is highly relied on operator’s experience. In this context, a reliable fully automatic segmentation method for the brain tumor segmentation is necessary for an efficient measurement of the tumor extent. In this study, we propose a fully automatic method for brain tumor segmentation, which is developed using U-Net based deep convolutional networks. Our method was evaluated on Multimodal Brain Tumor Image Segmentation (BRATS 2015) datasets, which contain 220 high-grade brain tumor and 54 low-grade tumor cases. Cross-validation has shown that our method can obtain promising segmentation efficiently.

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Literatur
1.
Zurück zum Zitat Schwartzbaum, J.A., Fisher, J.L., Aldape, K.D., Wrensch, M.: Epidemiology and molecular pathology of glioma. Nat. Clin. Pract. Neurol. 2, 494–503 (2006)CrossRef Schwartzbaum, J.A., Fisher, J.L., Aldape, K.D., Wrensch, M.: Epidemiology and molecular pathology of glioma. Nat. Clin. Pract. Neurol. 2, 494–503 (2006)CrossRef
2.
Zurück zum Zitat Smoll, N.R., Schaller, K., Gautschi, O.P.: Long-term survival of patients with glioblastoma multiforme (GBM). J. Clin. Neurosci. 20, 670–675 (2013)CrossRef Smoll, N.R., Schaller, K., Gautschi, O.P.: Long-term survival of patients with glioblastoma multiforme (GBM). J. Clin. Neurosci. 20, 670–675 (2013)CrossRef
3.
Zurück zum Zitat Ramakrishna, R., Hebb, A., Barber, J., Rostomily, R., Silbergeld, D.: Outcomes in reoperated low-grade gliomas. Neurosurgery 77, 175–184 (2015)CrossRef Ramakrishna, R., Hebb, A., Barber, J., Rostomily, R., Silbergeld, D.: Outcomes in reoperated low-grade gliomas. Neurosurgery 77, 175–184 (2015)CrossRef
4.
Zurück zum Zitat Mazzara, G.P., Velthuizen, R.P., Pearlman, J.L., Greenberg, H.M., Wagner, H.: Brain tumor target volume determination for radiation treatment planning through automated MRI segmentation. Int. J. Radiat. Oncol. Biol. Phys. 59, 300–312 (2004)CrossRef Mazzara, G.P., Velthuizen, R.P., Pearlman, J.L., Greenberg, H.M., Wagner, H.: Brain tumor target volume determination for radiation treatment planning through automated MRI segmentation. Int. J. Radiat. Oncol. Biol. Phys. 59, 300–312 (2004)CrossRef
5.
Zurück zum Zitat Yamahara, T., Numa, Y., Oishi, T., Kawaguchi, T., Seno, T., Asai, A., Kawamoto, K.: Morphological and flow cytometric analysis of cell infiltration in glioblastoma: a comparison of autopsy brain and neuroimaging. Brain Tumor Pathol. 27, 81–87 (2010)CrossRef Yamahara, T., Numa, Y., Oishi, T., Kawaguchi, T., Seno, T., Asai, A., Kawamoto, K.: Morphological and flow cytometric analysis of cell infiltration in glioblastoma: a comparison of autopsy brain and neuroimaging. Brain Tumor Pathol. 27, 81–87 (2010)CrossRef
6.
Zurück zum Zitat Bauer, S., Wiest, R., Nolte, L.-P., Reyes, M.: A survey of MRI-based medical image analysis for brain tumor studies. Phys. Med. Biol. 58, R97–R129 (2013)CrossRef Bauer, S., Wiest, R., Nolte, L.-P., Reyes, M.: A survey of MRI-based medical image analysis for brain tumor studies. Phys. Med. Biol. 58, R97–R129 (2013)CrossRef
7.
Zurück zum Zitat Jones, T.L., Byrnes, T.J., Yang, G., Howe, F.A., Bell, B.A., Barrick, T.R.: Brain tumor classification using the diffusion tensor image segmentation (D-SEG) technique. Neuro. Oncol. 17, 466–476 (2014) Jones, T.L., Byrnes, T.J., Yang, G., Howe, F.A., Bell, B.A., Barrick, T.R.: Brain tumor classification using the diffusion tensor image segmentation (D-SEG) technique. Neuro. Oncol. 17, 466–476 (2014)
8.
Zurück zum Zitat Soltaninejad, M., Yang, G., Lambrou, T., Allinson, N., Jones, T.L., Barrick, T.R., Howe, F.A., Ye, X.: Automated brain tumour detection and segmentation using superpixel-based extremely randomized trees in FLAIR MRI. Int. J. Comput. Assist. Radiol. Surg. 12(2), 183–203 (2016)CrossRef Soltaninejad, M., Yang, G., Lambrou, T., Allinson, N., Jones, T.L., Barrick, T.R., Howe, F.A., Ye, X.: Automated brain tumour detection and segmentation using superpixel-based extremely randomized trees in FLAIR MRI. Int. J. Comput. Assist. Radiol. Surg. 12(2), 183–203 (2016)CrossRef
9.
Zurück zum Zitat Szilágyi, L., Lefkovits, L., Benyó, B.: Automatic brain tumor segmentation in multispectral MRI volumes using a fuzzy c-means cascade algorithm. In: 2015 12th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD), pp. 285–291 (2015) Szilágyi, L., Lefkovits, L., Benyó, B.: Automatic brain tumor segmentation in multispectral MRI volumes using a fuzzy c-means cascade algorithm. In: 2015 12th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD), pp. 285–291 (2015)
10.
Zurück zum Zitat Mei, P.A., de Carvalho Carneiro, C., Fraser, S.J., Min, L.L., Reis, F.: Analysis of neoplastic lesions in magnetic resonance imaging using self-organizing maps. J. Neurol. Sci. 359, 78–83 (2015)CrossRef Mei, P.A., de Carvalho Carneiro, C., Fraser, S.J., Min, L.L., Reis, F.: Analysis of neoplastic lesions in magnetic resonance imaging using self-organizing maps. J. Neurol. Sci. 359, 78–83 (2015)CrossRef
11.
Zurück zum Zitat Juan-Albarracín, J., Fuster-Garcia, E., Manjón, J.V., Robles, M., Aparici, F., Martí-Bonmatí, L., García-Gómez, J.M.: Automated glioblastoma segmentation based on a multiparametric structured unsupervised classification. PLoS ONE 10, e0125143 (2015)CrossRef Juan-Albarracín, J., Fuster-Garcia, E., Manjón, J.V., Robles, M., Aparici, F., Martí-Bonmatí, L., García-Gómez, J.M.: Automated glioblastoma segmentation based on a multiparametric structured unsupervised classification. PLoS ONE 10, e0125143 (2015)CrossRef
12.
Zurück zum Zitat Dhanasekaran, R.: Fuzzy clustering and deformable model for tumor segmentation on MRI brain image: a combined approach. Procedia Eng. 30, 327–333 (2012)CrossRef Dhanasekaran, R.: Fuzzy clustering and deformable model for tumor segmentation on MRI brain image: a combined approach. Procedia Eng. 30, 327–333 (2012)CrossRef
13.
Zurück zum Zitat Wu, W., Chen, A.Y.C., Zhao, L., Corso, J.J.: Brain tumor detection and segmentation in a CRF (conditional random fields) framework with pixel-pairwise affinity and superpixel-level features. Int. J. Comput. Assist. Radiol. Surg. 9(2), 241–253 (2013)CrossRef Wu, W., Chen, A.Y.C., Zhao, L., Corso, J.J.: Brain tumor detection and segmentation in a CRF (conditional random fields) framework with pixel-pairwise affinity and superpixel-level features. Int. J. Comput. Assist. Radiol. Surg. 9(2), 241–253 (2013)CrossRef
14.
Zurück zum Zitat Pinto, A., Pereira, S., Correia, H., Oliveira, J., Rasteiro, D.M.L.D., Silva, C.A.: Brain tumour segmentation based on extremely randomized forest with high-level features. In: 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 3037–3040 (2015) Pinto, A., Pereira, S., Correia, H., Oliveira, J., Rasteiro, D.M.L.D., Silva, C.A.: Brain tumour segmentation based on extremely randomized forest with high-level features. In: 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 3037–3040 (2015)
15.
Zurück zum Zitat Gotz, M., Weber, C., Blocher, J., Stieltjes, B., Meinzer, H., Maier-Hein, K.: Extremely randomized trees based brain tumor segmentation. In: Proceeding of BRATS Challenge-MICCAI (2014) Gotz, M., Weber, C., Blocher, J., Stieltjes, B., Meinzer, H., Maier-Hein, K.: Extremely randomized trees based brain tumor segmentation. In: Proceeding of BRATS Challenge-MICCAI (2014)
16.
Zurück zum Zitat Soltaninejad, M., Yang, G., Lambrou, T., Allinson, N., Jones, T.L., Barrick, T.R., Howe, F.A., Ye, X.: Automated brain tumour detection and segmentation using superpixel-based extremely randomized trees in FLAIR MRI. Int. J. Comput. Assist. Radiol. Surg. 12(2), 183–203 (2016)CrossRef Soltaninejad, M., Yang, G., Lambrou, T., Allinson, N., Jones, T.L., Barrick, T.R., Howe, F.A., Ye, X.: Automated brain tumour detection and segmentation using superpixel-based extremely randomized trees in FLAIR MRI. Int. J. Comput. Assist. Radiol. Surg. 12(2), 183–203 (2016)CrossRef
17.
Zurück zum Zitat Jafari, M., Kasaei, S.: Automatic brain tissue detection in MRI images using seeded region growing segmentation and neural network classification. Aust. J. Basic Appl. Sci. 5, 1066–1079 (2011) Jafari, M., Kasaei, S.: Automatic brain tissue detection in MRI images using seeded region growing segmentation and neural network classification. Aust. J. Basic Appl. Sci. 5, 1066–1079 (2011)
18.
Zurück zum Zitat Subbanna, N., Precup, D., Arbel, T.: Iterative multilevel MRF leveraging context and voxel information for brain tumour segmentation in MRI. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp. 400–405 (2014) Subbanna, N., Precup, D., Arbel, T.: Iterative multilevel MRF leveraging context and voxel information for brain tumour segmentation in MRI. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp. 400–405 (2014)
19.
Zurück zum Zitat Menze, B.H., Jakab, A., Bauer, S., Kalpathy-Cramer, J., Farahani, K., Kirby, J., Burren, Y., Porz, N., Slotboom, J., Wiest, R., Lanczi, L., Gerstner, E., Weber, M.-A., Arbel, T., Avants, B.B., Ayache, N., Buendia, P., Collins, D.L., Cordier, N., Corso, J.J., Criminisi, A., Das, T., Delingette, H., Demiralp, Ç., Durst, C.R., Dojat, M., Doyle, S., Festa, J., Forbes, F., Geremia, E., Glocker, B., Golland, P., Guo, X., Hamamci, A., Iftekharuddin, K.M., Jena, R., John, N.M., Konukoglu, E., Lashkari, D., Mariz, J.A., Meier, R., Pereira, S., Precup, D., Price, S.J., Raviv, T.R., Reza, S.M.S., Ryan, M., Sarikaya, D., Schwartz, L., Shin, H.-C., Shotton, J., Silva, C.A., Sousa, N., Subbanna, N.K., Szekely, G., Taylor, T.J., Thomas, O.M., Tustison, N.J., Unal, G., Vasseur, F., Wintermark, M., Ye, D.H., Zhao, L., Zhao, B., Zikic, D., Prastawa, M., Reyes, M., Van Leemput, K.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imaging 34, 1993–2024 (2015)CrossRef Menze, B.H., Jakab, A., Bauer, S., Kalpathy-Cramer, J., Farahani, K., Kirby, J., Burren, Y., Porz, N., Slotboom, J., Wiest, R., Lanczi, L., Gerstner, E., Weber, M.-A., Arbel, T., Avants, B.B., Ayache, N., Buendia, P., Collins, D.L., Cordier, N., Corso, J.J., Criminisi, A., Das, T., Delingette, H., Demiralp, Ç., Durst, C.R., Dojat, M., Doyle, S., Festa, J., Forbes, F., Geremia, E., Glocker, B., Golland, P., Guo, X., Hamamci, A., Iftekharuddin, K.M., Jena, R., John, N.M., Konukoglu, E., Lashkari, D., Mariz, J.A., Meier, R., Pereira, S., Precup, D., Price, S.J., Raviv, T.R., Reza, S.M.S., Ryan, M., Sarikaya, D., Schwartz, L., Shin, H.-C., Shotton, J., Silva, C.A., Sousa, N., Subbanna, N.K., Szekely, G., Taylor, T.J., Thomas, O.M., Tustison, N.J., Unal, G., Vasseur, F., Wintermark, M., Ye, D.H., Zhao, L., Zhao, B., Zikic, D., Prastawa, M., Reyes, M., Van Leemput, K.: The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans. Med. Imaging 34, 1993–2024 (2015)CrossRef
20.
Zurück zum Zitat Hsieh, T.M., Liu, Y.-M., Liao, C.-C., Xiao, F., Chiang, I.-J., Wong, J.-M.: Automatic segmentation of meningioma from non-contrasted brain MRI integrating fuzzy clustering and region growing. BMC Med. Inform. Decis. Mak. 11, 54 (2011)CrossRef Hsieh, T.M., Liu, Y.-M., Liao, C.-C., Xiao, F., Chiang, I.-J., Wong, J.-M.: Automatic segmentation of meningioma from non-contrasted brain MRI integrating fuzzy clustering and region growing. BMC Med. Inform. Decis. Mak. 11, 54 (2011)CrossRef
21.
Zurück zum Zitat Pereira, S., Pinto, A., Alves, V., Silva, C.A.: Brain tumor segmentation using convolutional neural networks in MRI images. IEEE Trans. Med. Imaging 35, 1240–1251 (2016)CrossRef Pereira, S., Pinto, A., Alves, V., Silva, C.A.: Brain tumor segmentation using convolutional neural networks in MRI images. IEEE Trans. Med. Imaging 35, 1240–1251 (2016)CrossRef
22.
Zurück zum Zitat 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 (2016)CrossRef 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 (2016)CrossRef
23.
Zurück zum Zitat 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)CrossRef 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)CrossRef
24.
Zurück zum Zitat 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). doi:10.1007/978-3-319-24574-4_28 CrossRef 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). doi:10.​1007/​978-3-319-24574-4_​28 CrossRef
25.
Zurück zum Zitat Milletari, F., Navab, N., Ahmadi, S.-A.: V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation. arXiv, pp. 1–11 (2016) Milletari, F., Navab, N., Ahmadi, S.-A.: V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation. arXiv, pp. 1–11 (2016)
26.
Zurück zum Zitat Simard, P.Y., Steinkraus, D., Platt, J.C.: Best practices for convolutional neural networks applied to visual document analysis. In: Proceedings of Seventh International Conference on Document Analysis and Recognition, pp. 958–963. IEEE Computer Society (2003) Simard, P.Y., Steinkraus, D., Platt, J.C.: Best practices for convolutional neural networks applied to visual document analysis. In: Proceedings of Seventh International Conference on Document Analysis and Recognition, pp. 958–963. IEEE Computer Society (2003)
27.
Zurück zum Zitat Long, J., Shelhamer, E., Darrell, T.: Fully convolutional networks for semantic segmentation. In: 2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 3431–3440. IEEE (2015) Long, J., Shelhamer, E., Darrell, T.: Fully convolutional networks for semantic segmentation. In: 2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 3431–3440. IEEE (2015)
28.
Zurück zum Zitat Drozdzal, M., Vorontsov, E., Chartrand, G., Kadoury, S., Pal, C.: The importance of skip connections in biomedical image segmentation. In: Carneiro, G., et al. (eds.) LABELS/DLMIA -2016. LNCS, vol. 10008, pp. 179–187. Springer, Cham (2016). doi:10.1007/978-3-319-46976-8_19 CrossRef Drozdzal, M., Vorontsov, E., Chartrand, G., Kadoury, S., Pal, C.: The importance of skip connections in biomedical image segmentation. In: Carneiro, G., et al. (eds.) LABELS/DLMIA -2016. LNCS, vol. 10008, pp. 179–187. Springer, Cham (2016). doi:10.​1007/​978-3-319-46976-8_​19 CrossRef
29.
Zurück zum Zitat Kingma, D., Ba, J.: Adam: A Method for Stochastic Optimization (2014) Kingma, D., Ba, J.: Adam: A Method for Stochastic Optimization (2014)
Metadaten
Titel
Automatic Brain Tumor Detection and Segmentation Using U-Net Based Fully Convolutional Networks
verfasst von
Hao Dong
Guang Yang
Fangde Liu
Yuanhan Mo
Yike Guo
Copyright-Jahr
2017
DOI
https://doi.org/10.1007/978-3-319-60964-5_44

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