Skip to main content

2018 | OriginalPaper | Buchkapitel

3D Deep Neural Network-Based Brain Tumor Segmentation Using Multimodality Magnetic Resonance Sequences

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

Brain tumor segmentation plays a pivotal role in clinical practice and research settings. In this paper, we propose a 3D deep neural network-based algorithm for joint brain tumor detection and intra-tumor structure segmentation, including necrosis, edema, non-enhancing and enhancing tumor, using multimodal magnetic resonance imaging sequences. An ensemble of cascaded U-Nets is designed to detect the tumor and a deep convolutional neural network is constructed for patch-based intra-tumor structure segmentation. This algorithm has been evaluated on the BraTS 2017 Challenge dataset and achieved Dice similarity coefficients of 0.81, 0.69 and 0.55 in the segmentation of whole tumor, core tumor and enhancing tumor, respectively. Our results suggest that the proposed algorithm has promising performance in automated brain tumor segmentation.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literatur
1.
Zurück zum Zitat Mcguire, S.: World cancer report 2014. Geneva, Switzerland: world health organization, international agency for research on cancer, WHO Press, 2015. Adva. Nutr. 7, 418–419 (2016)CrossRef Mcguire, S.: World cancer report 2014. Geneva, Switzerland: world health organization, international agency for research on cancer, WHO Press, 2015. Adva. Nutr. 7, 418–419 (2016)CrossRef
2.
Zurück zum Zitat Agn, M., Puonti, O., Rosenschöld, P.M., Law, I., Van Leemput, K.: Brain tumor segmentation using a generative model with an RBM prior on tumor shape. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Handels, H. (eds.) BrainLes 2015. LNCS, vol. 9556, pp. 168–180. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-30858-6_15 CrossRef Agn, M., Puonti, O., Rosenschöld, P.M., Law, I., Van Leemput, K.: Brain tumor segmentation using a generative model with an RBM prior on tumor shape. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Handels, H. (eds.) BrainLes 2015. LNCS, vol. 9556, pp. 168–180. Springer, Cham (2016). https://​doi.​org/​10.​1007/​978-3-319-30858-6_​15 CrossRef
3.
Zurück zum Zitat Cordier, N., Delingette, H., Ayache, N.: A patch-based approach for the segmentation of pathologies: application to glioma labelling. IEEE Trans. Med. Imaging 35, 1066–1076 (2016)CrossRef Cordier, N., Delingette, H., Ayache, N.: A patch-based approach for the segmentation of pathologies: application to glioma labelling. IEEE Trans. Med. Imaging 35, 1066–1076 (2016)CrossRef
4.
Zurück zum Zitat Cobzas, D., Birkbeck, N., Schmidt, M.W., Jagersand, M., Murtha, A.: 3D variational brain tumor segmentation using a high dimensional feature set. In: International Conference on Computer Vision, pp. 1–8 (2007) Cobzas, D., Birkbeck, N., Schmidt, M.W., Jagersand, M., Murtha, A.: 3D variational brain tumor segmentation using a high dimensional feature set. In: International Conference on Computer Vision, pp. 1–8 (2007)
5.
Zurück zum Zitat Gooya, A., Pohl, K.M., Bilello, M., Cirillo, L., Biros, G., Melhem, E.R., Davatzikos, C.: GLISTR: glioma image segmentation and registration. IEEE Trans. Med. Imaging 31, 1941–1954 (2012)CrossRef Gooya, A., Pohl, K.M., Bilello, M., Cirillo, L., Biros, G., Melhem, E.R., Davatzikos, C.: GLISTR: glioma image segmentation and registration. IEEE Trans. Med. Imaging 31, 1941–1954 (2012)CrossRef
6.
Zurück zum Zitat Bauer, S., Nolte, L.-P., Reyes, M.: Fully automatic segmentation of brain tumor images using support vector machine classification in combination with hierarchical conditional random field regularization. In: Fichtinger, G., Martel, A., Peters, T. (eds.) MICCAI 2011. LNCS, vol. 6893, pp. 354–361. Springer, Heidelberg (2011). https://doi.org/10.1007/978-3-642-23626-6_44 CrossRef Bauer, S., Nolte, L.-P., Reyes, M.: Fully automatic segmentation of brain tumor images using support vector machine classification in combination with hierarchical conditional random field regularization. In: Fichtinger, G., Martel, A., Peters, T. (eds.) MICCAI 2011. LNCS, vol. 6893, pp. 354–361. Springer, Heidelberg (2011). https://​doi.​org/​10.​1007/​978-3-642-23626-6_​44 CrossRef
8.
Zurück zum Zitat Tustison, N.J., Shrinidhi, K.L., Wintermark, M., Durst, C.R., Kandel, B.M., Gee, J.C., Grossman, M.C., Avants, B.B.: Optimal symmetric multimodal templates and concatenated random forests for supervised brain tumor segmentation (simplified) with ANTsR. Neuroinformatics 13, 209–225 (2015)CrossRef Tustison, N.J., Shrinidhi, K.L., Wintermark, M., Durst, C.R., Kandel, B.M., Gee, J.C., Grossman, M.C., Avants, B.B.: Optimal symmetric multimodal templates and concatenated random forests for supervised brain tumor segmentation (simplified) with ANTsR. Neuroinformatics 13, 209–225 (2015)CrossRef
9.
Zurück zum Zitat Havaei, M., Davy, A., Wardefarley, D., Biard, A., Courville, A.C., Bengio, Y., Pal, C., Jodoin, P., Larochelle, H.: Brain tumor segmentation with deep neural networks. Med. Image Anal. 35, 18–31 (2017)CrossRef Havaei, M., Davy, A., Wardefarley, D., Biard, A., Courville, A.C., Bengio, Y., Pal, C., Jodoin, P., Larochelle, H.: Brain tumor segmentation with deep neural networks. Med. Image Anal. 35, 18–31 (2017)CrossRef
10.
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
11.
Zurück zum Zitat Zhao, L.Y., Jia, K.B.: Multiscale CNNs for brain tumor segmentation and diagnosis. Comput. Math. Methods Med. 2016, 1–7 (2016)MathSciNetCrossRef Zhao, L.Y., Jia, K.B.: Multiscale CNNs for brain tumor segmentation and diagnosis. Comput. Math. Methods Med. 2016, 1–7 (2016)MathSciNetCrossRef
12.
Zurück zum Zitat Konstantinos, K., Enzo, F., Sarah, P., Cristian, L., Aditya, N., Antonio, C., Daniel, R., Glocker, B.: DeepMedic on brain tumor segmentation. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Winzeck, S., Handels, H. (eds.) BrainLes 2016. LNCS, vol. 10154, pp. 138–149. Springer, Cham (2016) Konstantinos, K., Enzo, F., Sarah, P., Cristian, L., Aditya, N., Antonio, C., Daniel, R., Glocker, B.: DeepMedic on brain tumor segmentation. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Winzeck, S., Handels, H. (eds.) BrainLes 2016. LNCS, vol. 10154, pp. 138–149. Springer, Cham (2016)
13.
Zurück zum Zitat Zhao, X., Wu, Y., Song, G., Li, Z., Fan, Y., Zhang, Y.: Brain tumor segmentation using a fully convolutional neural network with conditional random fields. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Winzeck, S., Handels, H. (eds.) BrainLes 2016, vol. 10154, pp. 75–87. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-55524-9_8 CrossRef Zhao, X., Wu, Y., Song, G., Li, Z., Fan, Y., Zhang, Y.: Brain tumor segmentation using a fully convolutional neural network with conditional random fields. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Winzeck, S., Handels, H. (eds.) BrainLes 2016, vol. 10154, pp. 75–87. Springer, Cham (2016). https://​doi.​org/​10.​1007/​978-3-319-55524-9_​8 CrossRef
14.
Zurück zum Zitat Dong, H., Yang, G., Liu, F., Mo, Y., Guo Y.: Automatic brain tumor detection and segmentation using U-Net based fully convolutional networks. In: MIUA (2017) Dong, H., Yang, G., Liu, F., Mo, Y., Guo Y.: Automatic brain tumor detection and segmentation using U-Net based fully convolutional networks. In: MIUA (2017)
15.
Zurück zum Zitat Pereira, S., Oliveira, A., Alves, V., Silva, C.: On hierarchical brain tumor segmentation in MRI using fully convolutional neural networks: a preliminary study. In: 2017 IEEE 5th Portuguese Meeting on Bioengineering Pereira, S., Oliveira, A., Alves, V., Silva, C.: On hierarchical brain tumor segmentation in MRI using fully convolutional neural networks: a preliminary study. In: 2017 IEEE 5th Portuguese Meeting on Bioengineering
17.
Zurück zum Zitat Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J.S., Freymann, J.B., Farahani, K., Davatzikos, C.: Advancing the cancer genome Atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4 (2017). https://doi.org/10.1038/sdata.2017.117 Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J.S., Freymann, J.B., Farahani, K., Davatzikos, C.: Advancing the cancer genome Atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4 (2017). https://​doi.​org/​10.​1038/​sdata.​2017.​117
20.
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., 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(10), 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., 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(10), 1993–2024 (2015)CrossRef
21.
Zurück zum Zitat Ronneberger, O., Fischer, P., Brox, T.: U-Net: convolutional networks for biomedical image segmentation. In: International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 234–241 (2015) Ronneberger, O., Fischer, P., Brox, T.: U-Net: convolutional networks for biomedical image segmentation. In: International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 234–241 (2015)
22.
Metadaten
Titel
3D Deep Neural Network-Based Brain Tumor Segmentation Using Multimodality Magnetic Resonance Sequences
verfasst von
Yan Hu
Yong Xia
Copyright-Jahr
2018
DOI
https://doi.org/10.1007/978-3-319-75238-9_36