Skip to main content

2018 | OriginalPaper | Buchkapitel

Multimodal Brain Tumor Segmentation Using 3D Convolutional Networks

verfasst von : R. G. Rodríguez Colmeiro, C. A. Verrastro, T. Grosges

Erschienen in: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries

Verlag: Springer International Publishing

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

search-config
loading …

Abstract

Volume segmentation is one of the most time consuming and therefore error prone tasks in the field of medicine. The construction of a good segmentation requires cross-validation from highly trained professionals. In order to address this problem we propose the use of 3D deep convolutional networks (DCN). Using a 2 step procedure we first segment whole the tumor from a low resolution volume and then feed a second step which makes the fine tissue segmentation. The advantages of using 3D-DCN is that it extracts 3D features form all neighbouring voxels. In this method all parameters are self-learned during a single training procedure and its accuracy can improve by feeding new examples to the trained network. The training dice-loss value reach 0.85 and 0.9 for the coarse and fine segmentation networks respectively. The obtained validation and testing mean dice for the Whole Tumor class are 0.86 and 0.82 respectively.

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 Foster, B., Bagci, U., Mansoor, A., Xu, Z., Mollura, D.J.: A review on segmentation of positron emission tomography images. Comput. Biol. Med. 50, 76–96 (2014)CrossRef Foster, B., Bagci, U., Mansoor, A., Xu, Z., Mollura, D.J.: A review on segmentation of positron emission tomography images. Comput. Biol. Med. 50, 76–96 (2014)CrossRef
2.
Zurück zum Zitat Schmidhuber, J.: Deep learning in neural networks: an overview. Neural Netw. 61, 85–117 (2015)CrossRef Schmidhuber, J.: Deep learning in neural networks: an overview. Neural Netw. 61, 85–117 (2015)CrossRef
3.
Zurück zum Zitat Liu, Y., Gadepalli, K., Norouzi, M., Dahl, G.E., Kohlberger, T., Boyko, A., Venugopalan, S., Timofeev, A., Nelson, P.Q., Corrado, G.S., et al.: Detecting cancer metastases on gigapixel pathology images (2017). arXiv preprint: arXiv:1703.02442 Liu, Y., Gadepalli, K., Norouzi, M., Dahl, G.E., Kohlberger, T., Boyko, A., Venugopalan, S., Timofeev, A., Nelson, P.Q., Corrado, G.S., et al.: Detecting cancer metastases on gigapixel pathology images (2017). arXiv preprint: arXiv:​1703.​02442
4.
Zurück zum Zitat Anthimopoulos, M., Christodoulidis, S., Ebner, L., Christe, A., Mougiakakou, S.: Lung pattern classification for interstitial lung diseases using a deep convolutional neural network. IEEE Trans. Med. Imaging 35(5), 1207–1216 (2016)CrossRef Anthimopoulos, M., Christodoulidis, S., Ebner, L., Christe, A., Mougiakakou, S.: Lung pattern classification for interstitial lung diseases using a deep convolutional neural network. IEEE Trans. Med. Imaging 35(5), 1207–1216 (2016)CrossRef
5.
Zurück zum Zitat Kim, B.-C., Sung, Y.S., Suk, H.-I.: Deep feature learning for pulmonary nodule classification in a lung CT. In: 2016 4th International Winter Conference on Brain-Computer Interface (BCI), pp. 1–3. IEEE (2016) Kim, B.-C., Sung, Y.S., Suk, H.-I.: Deep feature learning for pulmonary nodule classification in a lung CT. In: 2016 4th International Winter Conference on Brain-Computer Interface (BCI), pp. 1–3. IEEE (2016)
6.
Zurück zum Zitat Gao, X.W., Hui, R.: A deep learning based approach to classification of CT brain images (2016) Gao, X.W., Hui, R.: A deep learning based approach to classification of CT brain images (2016)
7.
Zurück zum Zitat Roth, H.R., Lee, C.T., Shin, H.-C., Seff, A., Kim, L., Yao, J., Lu, L., Summers, R.M.: Anatomy-specific classification of medical images using deep convolutional nets. In: 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI), pp. 101–104. IEEE (2015) Roth, H.R., Lee, C.T., Shin, H.-C., Seff, A., Kim, L., Yao, J., Lu, L., Summers, R.M.: Anatomy-specific classification of medical images using deep convolutional nets. In: 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI), pp. 101–104. IEEE (2015)
9.
Zurück zum Zitat Çiçek, Ö., Abdulkadir, A., Lienkamp, S.S., Brox, T., Ronneberger, O.: 3D U-Net: learning dense volumetric segmentation from sparse annotation. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016, Part II. LNCS, vol. 9901, pp. 424–432. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46723-8_49 CrossRef Çiçek, Ö., Abdulkadir, A., Lienkamp, S.S., Brox, T., Ronneberger, O.: 3D U-Net: learning dense volumetric segmentation from sparse annotation. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016, Part II. LNCS, vol. 9901, pp. 424–432. Springer, Cham (2016). https://​doi.​org/​10.​1007/​978-3-319-46723-8_​49 CrossRef
10.
Zurück zum Zitat Milletari, F., Navab, N., Ahmadi, S.-A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: 2016 Fourth International Conference on 3D Vision (3DV), pp. 565–571. IEEE (2016) Milletari, F., Navab, N., Ahmadi, S.-A.: V-net: fully convolutional neural networks for volumetric medical image segmentation. In: 2016 Fourth International Conference on 3D Vision (3DV), pp. 565–571. IEEE (2016)
11.
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 (2017)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 (2017)CrossRef
12.
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(5), 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(5), 1240–1251 (2016)CrossRef
13.
Zurück zum Zitat 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) 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)
14.
Zurück zum Zitat Chang, P.D.: Fully convolutional deep residual neural networks for brain tumor segmentation. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Winzeck, S., Handels, H. (eds.) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. LNCS, vol. 10154, pp. 108–118. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-55524-9_11 CrossRef Chang, P.D.: Fully convolutional deep residual neural networks for brain tumor segmentation. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Winzeck, S., Handels, H. (eds.) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. LNCS, vol. 10154, pp. 108–118. Springer, Cham (2016). https://​doi.​org/​10.​1007/​978-3-319-55524-9_​11 CrossRef
15.
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. Nat. Sci. Data 4, 170117 (2017)CrossRef 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. Nat. Sci. Data 4, 170117 (2017)CrossRef
19.
Zurück zum Zitat Ioffe, S., Szegedy, C.: Batch normalization: Accelerating deep network training by reducing internal covariate shift (2015). arXiv preprint: arXiv:1502.03167 Ioffe, S., Szegedy, C.: Batch normalization: Accelerating deep network training by reducing internal covariate shift (2015). arXiv preprint: arXiv:​1502.​03167
20.
Zurück zum Zitat del Fresno, M., Vénere, M., Clausse, A.: A combined region growing and deformable model method for extraction of closed surfaces in 3D CT and MRI scans. Comput. Med. Imaging Graph. 33(5), 369–376 (2009)CrossRef del Fresno, M., Vénere, M., Clausse, A.: A combined region growing and deformable model method for extraction of closed surfaces in 3D CT and MRI scans. Comput. Med. Imaging Graph. 33(5), 369–376 (2009)CrossRef
21.
Zurück zum Zitat Grosges, T., Borouchaki, H., Barchiési, D.: New adaptive mesh development for accurate near-field enhancement computation. J. Microsc. 229(2), 293–301 (2008)MathSciNetCrossRef Grosges, T., Borouchaki, H., Barchiési, D.: New adaptive mesh development for accurate near-field enhancement computation. J. Microsc. 229(2), 293–301 (2008)MathSciNetCrossRef
Metadaten
Titel
Multimodal Brain Tumor Segmentation Using 3D Convolutional Networks
verfasst von
R. G. Rodríguez Colmeiro
C. A. Verrastro
T. Grosges
Copyright-Jahr
2018
DOI
https://doi.org/10.1007/978-3-319-75238-9_20