Skip to main content

Over-and-Under Complete Convolutional RNN for MRI Reconstruction

  • Conference paper
  • First Online:
Medical Image Computing and Computer Assisted Intervention – MICCAI 2021 (MICCAI 2021)

Abstract

Reconstructing magnetic resonance (MR) images from under-sampled data is a challenging problem due to various artifacts introduced by the under-sampling operation. Recent deep learning-based methods for MR image reconstruction usually leverage a generic auto-encoder architecture which captures low-level features at the initial layers and high-level features at the deeper layers. Such networks focus much on global features which may not be optimal to reconstruct the fully-sampled image. In this paper, we propose an Over-and-Under Complete Convolutional Recurrent Neural Network (OUCR), which consists of an overcomplete and an undercomplete Convolutional Recurrent Neural Network (CRNN). The overcomplete branch gives special attention in learning local structures by restraining the receptive field of the network. Combining it with the undercomplete branch leads to a network which focuses more on low-level features without losing out on the global structures. Extensive experiments on two datasets demonstrate that the proposed method achieves significant improvements over the compressed sensing and popular deep learning-based methods with less number of trainable parameters.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Akçakaya, M., Moeller, S., Weingärtner, S., Uğurbil, K.: Scan-specific robust artificial-neural-networks for k-space interpolation (RAKI) reconstruction: database-free deep learning for fast imaging. Magn. Reson. Med. 81(1), 439–453 (2019)

    Article  Google Scholar 

  2. Chen, E.Z., Chen, T., Sun, S.: MRI image reconstruction via learning optimization using neural ODEs. In: Martel, A.L., et al. (eds.) MICCAI 2020. LNCS, vol. 12262, pp. 83–93. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-59713-9_9

    Chapter  Google Scholar 

  3. Edmund, J.M., Nyholm, T.: A review of substitute CT generation for MRI-only radiation therapy. Radiat. Oncol. 12(1), 1–15 (2017)

    Article  Google Scholar 

  4. Eo, T., Jun, Y., Kim, T., Jang, J., Lee, H.J., Hwang, D.: Kiki-net: cross-domain convolutional neural networks for reconstructing undersampled magnetic resonance images. Magn. Reson. Med. 80(5), 2188–2201 (2018)

    Article  Google Scholar 

  5. Fisher, R.B.: Cvonline: The evolving, distributed, non-proprietary, on-line compendium of computer vision (2008). https://homepages.inf.ed.ac.uk/rbf/CVonline. Accessed 28 Jan 2006

  6. Guo, P., Wang, P., Yasarla, R., Zhou, J., Patel, V.M., Jiang, S.: Anatomic and molecular MR image synthesis using confidence guided CNNS. IEEE Trans. Med. Imaging, 1 (2020). https://doi.org/10.1109/TMI.2020.3046460

  7. Guo, P., Wang, P., Zhou, J., Jiang, S., Patel, V.M.: Multi-institutional collaborations for improving deep learning-based magnetic resonance image reconstruction using federated learning. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), pp. 2423–2432 (2021)

    Google Scholar 

  8. Guo, P., Wang, P., Zhou, J., Patel, V.M., Jiang, S.: Lesion mask-based simultaneous synthesis of anatomic and molecular MR Images Using a GAN. In: Martel, A.L., et al. (eds.) MICCAI 2020. LNCS, vol. 12262, pp. 104–113. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-59713-9_11

    Chapter  Google Scholar 

  9. Haldar, J.P., Hernando, D., Liang, Z.P.: Compressed-sensing MRI with random encoding. IEEE Trans. Med. Imaging 30(4), 893–903 (2010)

    Article  Google Scholar 

  10. Jiang, S., et al.: Identifying recurrent malignant glioma after treatment using amide proton transfer-weighted MR imaging: a validation study with image-guided stereotactic biopsy. Clin. Cancer Res. 25(2), 552–561 (2019)

    Article  Google Scholar 

  11. Knoll, F., et al.: fastmri: A publicly available raw k-space and DICOM dataset of knee images for accelerated MR image reconstruction using machine learning. Radiol. Artif. Intell. 2(1), e190007 (2020)

    Google Scholar 

  12. Lee, D., Yoo, J., Tak, S., Ye, J.C.: Deep residual learning for accelerated MRI using magnitude and phase networks. IEEE Trans. Biomed. Eng. 65(9), 1985–1995 (2018)

    Article  Google Scholar 

  13. Lewicki, M.S., Sejnowski, T.J.: Learning overcomplete representations. Neural Comput. 12(2), 337–365 (2000)

    Article  Google Scholar 

  14. Liang, D., Cheng, J., Ke, Z., Ying, L.: Deep magnetic resonance image reconstruction: inverse problems meet neural networks. IEEE Sign. Process. Mag. 37(1), 141–151 (2020)

    Article  Google Scholar 

  15. Liang, D., Liu, B., Wang, J., Ying, L.: Accelerating sense using compressed sensing. Magn. Reson. Med. Offic. J. Int. Soc. Magn. Reson. Med. 62(6), 1574–1584 (2009)

    Article  Google Scholar 

  16. Majumdar, A.: Improving synthesis and analysis prior blind compressed sensing with low-rank constraints for dynamic MRI reconstruction. Magn. Reson. Imaging 33(1), 174–179 (2015)

    Article  Google Scholar 

  17. Mezrich, R.: A perspective on k-space. Radiology 195(2), 297–315 (1995)

    Article  Google Scholar 

  18. Patel, V.M., Chellappa, R.: Sparse representations, compressive sensing and dictionaries for pattern recognition. In: The First Asian Conference on Pattern Recognition, pp. 325–329. IEEE (2011)

    Google Scholar 

  19. Patel, V.M., Maleh, R., Gilbert, A.C., Chellappa, R.: Gradient-based image recovery methods from incomplete fourier measurements. IEEE Trans. Image Process. 21(1), 94–105 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  20. Pruessmann, K.P., Weiger, M., Scheidegger, M.B., Boesiger, P.: Sense: sensitivity encoding for fast MRI. Magn. Reson. Med. Offic. J. Int. Soc. Magn. Reson. Med. 42(5), 952–962 (1999)

    Article  Google Scholar 

  21. Putzky, P., Welling, M.: Invert to learn to invert. arXiv preprint arXiv:1911.10914 (2019)

  22. Qin, C., et al.: Convolutional recurrent neural networks for dynamic MR image reconstruction. IEEE Trans. Med. Imaging 38(1), 280–290 (2019). https://doi.org/10.1109/TMI.2018.2863670

    Article  MathSciNet  Google Scholar 

  23. Ravishankar, S., Bresler, Y.: MR image reconstruction from highly undersampled k-space data by dictionary learning. IEEE Trans. Med. Imaging 30(5), 1028–1041 (2010)

    Article  Google Scholar 

  24. 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

    Chapter  Google Scholar 

  25. Schlemper, J., et al.: A deep cascade of convolutional neural networks for dynamic MR image reconstruction. IEEE Trans. Med. Imaging 37(2), 491–503 (2017)

    Article  Google Scholar 

  26. Tamir, J.I., Ong, F., Cheng, J.Y., Uecker, M., Lustig, M.: Generalized magnetic resonance image reconstruction using the Berkeley advanced reconstruction toolbox. In: ISMRM Workshop on Data Sampling & Image Reconstruction, Sedona, AZ (2016)

    Google Scholar 

  27. Valanarasu, J.M.J., Patel, V.M.: Overcomplete deep subspace clustering networks. In: Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision, pp. 746–755 (2021)

    Google Scholar 

  28. Valanarasu, J.M.J., Sindagi, V.A., Hacihaliloglu, I., Patel, V.M.: Kiu-net: overcomplete convolutional architectures for biomedical image and volumetric segmentation. arXiv preprint arXiv:2010.01663 (2020)

  29. Valanarasu, J.M.J., Sindagi, V.A., Hacihaliloglu, I., Patel, V.M.: KiU-Net: towards accurate segmentation of biomedical images using over-complete representations. In: Martel, A.L., et al. (eds.) MICCAI 2020. LNCS, vol. 12264, pp. 363–373. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-59719-1_36

    Chapter  Google Scholar 

  30. Vincent, P., Larochelle, H., Bengio, Y., Manzagol, P.A.: Extracting and composing robust features with denoising autoencoders. In: Proceedings of the 25th International Conference on Machine Learning, pp. 1096–1103 (2008)

    Google Scholar 

  31. Wang, P., Chen, E.Z., Chen, T., Patel, V.M., Sun, S.: Pyramid convolutional RNN for MRI reconstruction. arXiv preprint arXiv:1912.00543 (2019)

  32. Yasarla, R., Valanarasu, J.M.J., Patel, V.M.: Exploring overcomplete representations for single image deraining using CNNS. IEEE J. Select. Top. Sign. Process. 15(2), 229–239 (2020)

    Google Scholar 

Download references

Acknowledgment

This work was supported by grants from the National Science Foundation (1910141) and the National Institutes of Health (R37CA248077).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Pengfei Guo .

Editor information

Editors and Affiliations

1 Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (pdf 215 KB)

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Guo, P., Valanarasu, J.M.J., Wang, P., Zhou, J., Jiang, S., Patel, V.M. (2021). Over-and-Under Complete Convolutional RNN for MRI Reconstruction. In: de Bruijne, M., et al. Medical Image Computing and Computer Assisted Intervention – MICCAI 2021. MICCAI 2021. Lecture Notes in Computer Science(), vol 12906. Springer, Cham. https://doi.org/10.1007/978-3-030-87231-1_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-87231-1_2

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-87230-4

  • Online ISBN: 978-3-030-87231-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics