Skip to main content

2016 | OriginalPaper | Buchkapitel

Whole Image Synthesis Using a Deep Encoder-Decoder Network

verfasst von : Vasileios Sevetlidis, Mario Valerio Giuffrida, Sotirios A. Tsaftaris

Erschienen in: Simulation and Synthesis in Medical Imaging

Verlag: Springer International Publishing

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

search-config
loading …

Abstract

The synthesis of medical images is an intensity transformation of a given modality in a way that represents an acquisition with a different modality (in the context of MRI this represents the synthesis of images originating from different MR sequences). Most methods follow a patch-based approach, which is computationally inefficient during synthesis and requires some sort of ‘fusion’ to synthesize a whole image from patch-level results. In this paper, we present a whole image synthesis approach that relies on deep neural networks. Our architecture resembles those of encoder-decoder networks, which aims to synthesize a source MRI modality to an other target MRI modality. The proposed method is computationally fast, it doesn’t require extensive amounts of memory, and produces comparable results to recent patch-based approaches.

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!

Fußnoten
1
There is also the recent exciting unsupervised work by [24], however for ease of introducing the reader to the topic this is not discussed here.
 
2
Freely available at https://​github.​com/​rasmusbergpalm/​DeepLearnToolbox​ [18]. We modified the current implementation to enable also GPU (CUDA) processing.
 
3
We use only the CPU and not GPU to permit fair comparison with our MP implementation which does not use GPU.
 
Literatur
1.
Zurück zum Zitat Alexander, D.C., Zikic, D., Zhang, J., Zhang, H., Criminisi, A.: Image quality transfer via random forest regression: applications in diffusion MRI. In: Golland, P., Hata, N., Barillot, C., Hornegger, J., Howe, R. (eds.) MICCAI 2014, Part III. LNCS, vol. 8675, pp. 225–232. Springer, Heidelberg (2014) Alexander, D.C., Zikic, D., Zhang, J., Zhang, H., Criminisi, A.: Image quality transfer via random forest regression: applications in diffusion MRI. In: Golland, P., Hata, N., Barillot, C., Hornegger, J., Howe, R. (eds.) MICCAI 2014, Part III. LNCS, vol. 8675, pp. 225–232. Springer, Heidelberg (2014)
2.
Zurück zum Zitat Artaechevarria, X., Munoz-Barrutia, A., Ortiz-de-Solórzano, C.: Combination strategies in multi-atlas image segmentation: application to brain MR data. IEEE Trans. Med. Imaging 28(8), 1266–1277 (2009)CrossRef Artaechevarria, X., Munoz-Barrutia, A., Ortiz-de-Solórzano, C.: Combination strategies in multi-atlas image segmentation: application to brain MR data. IEEE Trans. Med. Imaging 28(8), 1266–1277 (2009)CrossRef
3.
Zurück zum Zitat Burgos, N., Cardoso, M.J., Thielemans, K., Modat, M., Pedemonte, S., Dickson, J., Barnes, A., Ahmed, R., Mahoney, C.J., Schott, J.M., et al.: Attenuation correction synthesis for hybrid PET-MR scanners: application to brain studies. IEEE Trans. Med. Imaging 33(12), 2332–2341 (2014)CrossRef Burgos, N., Cardoso, M.J., Thielemans, K., Modat, M., Pedemonte, S., Dickson, J., Barnes, A., Ahmed, R., Mahoney, C.J., Schott, J.M., et al.: Attenuation correction synthesis for hybrid PET-MR scanners: application to brain studies. IEEE Trans. Med. Imaging 33(12), 2332–2341 (2014)CrossRef
4.
Zurück zum Zitat Cardoso, M.J., Sudre, C.H., Modat, M., Ourselin, S.: Template-based multimodal joint generative model of brain data. In: Ourselin, S., Alexander, D.C., Westin, C.-F., Cardoso, M.J. (eds.) IPMI 2015. LNCS, vol. 9123, pp. 17–29. Springer, Heidelberg (2015). doi:10.1007/978-3-319-19992-4_2 CrossRef Cardoso, M.J., Sudre, C.H., Modat, M., Ourselin, S.: Template-based multimodal joint generative model of brain data. In: Ourselin, S., Alexander, D.C., Westin, C.-F., Cardoso, M.J. (eds.) IPMI 2015. LNCS, vol. 9123, pp. 17–29. Springer, Heidelberg (2015). doi:10.​1007/​978-3-319-19992-4_​2 CrossRef
5.
Zurück zum Zitat Cho, K.H., Ilin, A., Raiko, T.: Improved learning of Gaussian-Bernoulli restricted Boltzmann machines. In: Honkela, T., Duch, W., Girolami, M., Kaski, S. (eds.) ICANN 2011. LNCS, vol. 6791, pp. 10–17. Springer, Heidelberg (2011). doi:10.1007/978-3-642-21735-7_2 CrossRef Cho, K.H., Ilin, A., Raiko, T.: Improved learning of Gaussian-Bernoulli restricted Boltzmann machines. In: Honkela, T., Duch, W., Girolami, M., Kaski, S. (eds.) ICANN 2011. LNCS, vol. 6791, pp. 10–17. Springer, Heidelberg (2011). doi:10.​1007/​978-3-642-21735-7_​2 CrossRef
6.
Zurück zum Zitat Fischl, B., Salat, D.H., van der Kouwe, A.J., Makris, N., Ségonne, F., Quinn, B.T., Dale, A.M.: Sequence-independent segmentation of magnetic resonance images. Neuroimage 23, S69–S84 (2004)CrossRef Fischl, B., Salat, D.H., van der Kouwe, A.J., Makris, N., Ségonne, F., Quinn, B.T., Dale, A.M.: Sequence-independent segmentation of magnetic resonance images. Neuroimage 23, S69–S84 (2004)CrossRef
7.
Zurück zum Zitat Guimond, A., Roche, A., Ayache, N., Meunier, J.: Three-dimensional multimodal brain warping using the demons algorithm and adaptive intensity corrections. IEEE Trans. Med. Imaging 20(1), 58–69 (2001)CrossRef Guimond, A., Roche, A., Ayache, N., Meunier, J.: Three-dimensional multimodal brain warping using the demons algorithm and adaptive intensity corrections. IEEE Trans. Med. Imaging 20(1), 58–69 (2001)CrossRef
8.
Zurück zum Zitat Hertzmann, A., Jacobs, C.E., Oliver, N., Curless, B., Salesin, D.H.: Image analogies. In: Proceedings of the 28th Annual Conference on Computer Graphics and Interactive Techniques, pp. 327–340. ACM (2001) Hertzmann, A., Jacobs, C.E., Oliver, N., Curless, B., Salesin, D.H.: Image analogies. In: Proceedings of the 28th Annual Conference on Computer Graphics and Interactive Techniques, pp. 327–340. ACM (2001)
9.
10.
Zurück zum Zitat Hinton, G.E., Osindero, S., Teh, Y.W.: A fast learning algorithm for deep belief nets. Neural Comput. 18(7), 1527–1554 (2006)MathSciNetCrossRefMATH Hinton, G.E., Osindero, S., Teh, Y.W.: A fast learning algorithm for deep belief nets. Neural Comput. 18(7), 1527–1554 (2006)MathSciNetCrossRefMATH
11.
Zurück zum Zitat Iglesias, J.E., Konukoglu, E., Zikic, D., Glocker, B., Van Leemput, K., Fischl, B.: Is synthesizing MRI contrast useful for inter-modality analysis? In: Mori, K., Sakuma, I., Sato, Y., Barillot, C., Navab, N. (eds.) MICCAI 2013, Part I. LNCS, vol. 8149, pp. 631–638. Springer, Heidelberg (2013)CrossRef Iglesias, J.E., Konukoglu, E., Zikic, D., Glocker, B., Van Leemput, K., Fischl, B.: Is synthesizing MRI contrast useful for inter-modality analysis? In: Mori, K., Sakuma, I., Sato, Y., Barillot, C., Navab, N. (eds.) MICCAI 2013, Part I. LNCS, vol. 8149, pp. 631–638. Springer, Heidelberg (2013)CrossRef
12.
Zurück zum Zitat Jog, A., Roy, S., Carass, A., Prince, J.L.: Magnetic resonance image synthesis through patch regression. In: IEEE 10th ISBI, pp. 350–353. IEEE (2013) Jog, A., Roy, S., Carass, A., Prince, J.L.: Magnetic resonance image synthesis through patch regression. In: IEEE 10th ISBI, pp. 350–353. IEEE (2013)
13.
Zurück zum Zitat Kamyshanska, H., Memisevic, R.: The potential energy of an autoencoder. IEEE Trans. PAMI 37(6), 1261–1273 (2015)CrossRef Kamyshanska, H., Memisevic, R.: The potential energy of an autoencoder. IEEE Trans. PAMI 37(6), 1261–1273 (2015)CrossRef
14.
Zurück zum Zitat Konukoglu, E., van der Kouwe, A., Sabuncu, M.R., Fischl, B.: Example-based restoration of high-resolution magnetic resonance image acquisitions. In: Mori, K., Sakuma, I., Sato, Y., Barillot, C., Navab, N. (eds.) MICCAI 2013, Part I. LNCS, vol. 8149, pp. 131–138. Springer, Heidelberg (2013)CrossRef Konukoglu, E., van der Kouwe, A., Sabuncu, M.R., Fischl, B.: Example-based restoration of high-resolution magnetic resonance image acquisitions. In: Mori, K., Sakuma, I., Sato, Y., Barillot, C., Navab, N. (eds.) MICCAI 2013, Part I. LNCS, vol. 8149, pp. 131–138. Springer, Heidelberg (2013)CrossRef
15.
Zurück zum Zitat Kroon, D.J., Slump, C.H.: MRI modalitiy transformation in demon registration. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009, pp. 963–966. IEEE (2009) Kroon, D.J., Slump, C.H.: MRI modalitiy transformation in demon registration. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009, pp. 963–966. IEEE (2009)
16.
Zurück zum Zitat Larochelle, H., Erhan, D., Courville, A., Bergstra, J., Bengio, Y.: An empirical evaluation of deep architectures on problems with many factors of variation. In: Proceedings of the 24th ICML, pp. 473–480 (2007) Larochelle, H., Erhan, D., Courville, A., Bergstra, J., Bengio, Y.: An empirical evaluation of deep architectures on problems with many factors of variation. In: Proceedings of the 24th ICML, pp. 473–480 (2007)
17.
Zurück zum Zitat Maier, O., Wilms, M., von der Gablentz, J., Krämer, U.M., Münte, T.F., Handels, H.: Extra tree forests for sub-acute ischemic stroke lesion segmentation in MR sequences. J. Neurosci. Methods 240, 89–100 (2015)CrossRef Maier, O., Wilms, M., von der Gablentz, J., Krämer, U.M., Münte, T.F., Handels, H.: Extra tree forests for sub-acute ischemic stroke lesion segmentation in MR sequences. J. Neurosci. Methods 240, 89–100 (2015)CrossRef
18.
Zurück zum Zitat Palm, R.B.: Prediction as a candidate for learning deep hierarchical models of data. Master’s thesis (2012) Palm, R.B.: Prediction as a candidate for learning deep hierarchical models of data. Master’s thesis (2012)
19.
Zurück zum Zitat Rohlfing, T., Russakoff, D.B., Maurer, C.R.: Expectation maximization strategies for multi-atlas multi-label segmentation. In: Taylor, C.J., Noble, J.A. (eds.) IPMI 2003. LNCS, vol. 2732, pp. 210–221. Springer, Heidelberg (2003)CrossRef Rohlfing, T., Russakoff, D.B., Maurer, C.R.: Expectation maximization strategies for multi-atlas multi-label segmentation. In: Taylor, C.J., Noble, J.A. (eds.) IPMI 2003. LNCS, vol. 2732, pp. 210–221. Springer, Heidelberg (2003)CrossRef
20.
Zurück zum Zitat Rousseau, F.: Brain hallucination. In: Forsyth, D., Torr, P., Zisserman, A. (eds.) ECCV 2008, Part I. LNCS, vol. 5302, pp. 497–508. Springer, Heidelberg (2008)CrossRef Rousseau, F.: Brain hallucination. In: Forsyth, D., Torr, P., Zisserman, A. (eds.) ECCV 2008, Part I. LNCS, vol. 5302, pp. 497–508. Springer, Heidelberg (2008)CrossRef
21.
Zurück zum Zitat Roy, S., Carass, A., Prince, J.: A compressed sensing approach for MR tissue contrast synthesis. In: Székely, G., Hahn, H.K. (eds.) IPMI 2011. LNCS, vol. 6801, pp. 371–383. Springer, Heidelberg (2011)CrossRef Roy, S., Carass, A., Prince, J.: A compressed sensing approach for MR tissue contrast synthesis. In: Székely, G., Hahn, H.K. (eds.) IPMI 2011. LNCS, vol. 6801, pp. 371–383. Springer, Heidelberg (2011)CrossRef
22.
Zurück zum Zitat Tulder, G., Bruijne, M.: Why does synthesized data improve multi-sequence classification? In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9349, pp. 531–538. Springer, Heidelberg (2015). doi:10.1007/978-3-319-24553-9_65 CrossRef Tulder, G., Bruijne, M.: Why does synthesized data improve multi-sequence classification? In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9349, pp. 531–538. Springer, Heidelberg (2015). doi:10.​1007/​978-3-319-24553-9_​65 CrossRef
23.
Zurück zum Zitat Nguyen, H., Zhou, K., Vemulapalli, R.: Cross-domain synthesis of medical images using efficient location-sensitive deep network. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9349, pp. 677–684. Springer, Heidelberg (2015). doi:10.1007/978-3-319-24553-9_83 CrossRef Nguyen, H., Zhou, K., Vemulapalli, R.: Cross-domain synthesis of medical images using efficient location-sensitive deep network. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9349, pp. 677–684. Springer, Heidelberg (2015). doi:10.​1007/​978-3-319-24553-9_​83 CrossRef
24.
Zurück zum Zitat Vemulapalli, R., Van Nguyen, H., Zhou, S.K.: Unsupervised cross-modal synthesis of subject-specific scans. In: Proceedings of the IEEE ICCV, pp. 630–638 (2015) Vemulapalli, R., Van Nguyen, H., Zhou, S.K.: Unsupervised cross-modal synthesis of subject-specific scans. In: Proceedings of the IEEE ICCV, pp. 630–638 (2015)
25.
Zurück zum Zitat Vincent, P., Larochelle, H., Lajoie, I., Bengio, Y., Manzagol, P.A.: Stacked denoising autoencoders: learning useful representations in a deep network with a local denoising criterion. J. Mach. Learn. Res. 11, 3371–3408 (2010)MathSciNetMATH Vincent, P., Larochelle, H., Lajoie, I., Bengio, Y., Manzagol, P.A.: Stacked denoising autoencoders: learning useful representations in a deep network with a local denoising criterion. J. Mach. Learn. Res. 11, 3371–3408 (2010)MathSciNetMATH
26.
Zurück zum Zitat Wein, W., Brunke, S., Khamene, A., Callstrom, M.R., Navab, N.: Automatic CT-ultrasound registration for diagnostic imaging and image-guided intervention. Med. Image Anal. 12(5), 577–585 (2008)CrossRef Wein, W., Brunke, S., Khamene, A., Callstrom, M.R., Navab, N.: Automatic CT-ultrasound registration for diagnostic imaging and image-guided intervention. Med. Image Anal. 12(5), 577–585 (2008)CrossRef
27.
Zurück zum Zitat Williams, D., Hinton, G.: Learning representations by back-propagating errors. Nature 323, 533–536 (1986)CrossRef Williams, D., Hinton, G.: Learning representations by back-propagating errors. Nature 323, 533–536 (1986)CrossRef
28.
Zurück zum Zitat Wolz, R., Chu, C., Misawa, K., Mori, K., Rueckert, D.: Multi-organ abdominal CT segmentation using hierarchically weighted subject-specific atlases. In: Ayache, N., Delingette, H., Golland, P., Mori, K. (eds.) MICCAI 2012, Part I. LNCS, vol. 7510, pp. 10–17. Springer, Heidelberg (2012)CrossRef Wolz, R., Chu, C., Misawa, K., Mori, K., Rueckert, D.: Multi-organ abdominal CT segmentation using hierarchically weighted subject-specific atlases. In: Ayache, N., Delingette, H., Golland, P., Mori, K. (eds.) MICCAI 2012, Part I. LNCS, vol. 7510, pp. 10–17. Springer, Heidelberg (2012)CrossRef
29.
Zurück zum Zitat Ye, D.H., Zikic, D., Glocker, B., Criminisi, A., Konukoglu, E.: Modality propagation: coherent synthesis of subject-specific scans with data-driven regularization. In: Mori, K., Sakuma, I., Sato, Y., Barillot, C., Navab, N. (eds.) MICCAI 2013, Part I. LNCS, vol. 8149, pp. 606–613. Springer, Heidelberg (2013)CrossRef Ye, D.H., Zikic, D., Glocker, B., Criminisi, A., Konukoglu, E.: Modality propagation: coherent synthesis of subject-specific scans with data-driven regularization. In: Mori, K., Sakuma, I., Sato, Y., Barillot, C., Navab, N. (eds.) MICCAI 2013, Part I. LNCS, vol. 8149, pp. 606–613. Springer, Heidelberg (2013)CrossRef
Metadaten
Titel
Whole Image Synthesis Using a Deep Encoder-Decoder Network
verfasst von
Vasileios Sevetlidis
Mario Valerio Giuffrida
Sotirios A. Tsaftaris
Copyright-Jahr
2016
DOI
https://doi.org/10.1007/978-3-319-46630-9_13

Premium Partner