Papers
Topics
Authors
Recent
Gemini 2.5 Flash
Gemini 2.5 Flash
41 tokens/sec
GPT-4o
59 tokens/sec
Gemini 2.5 Pro Pro
41 tokens/sec
o3 Pro
7 tokens/sec
GPT-4.1 Pro
50 tokens/sec
DeepSeek R1 via Azure Pro
28 tokens/sec
2000 character limit reached

Deep Learning for Accelerated and Robust MRI Reconstruction: a Review (2404.15692v1)

Published 24 Apr 2024 in cs.LG and eess.IV

Abstract: Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction. It focuses on DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. These include end-to-end neural networks, pre-trained networks, generative models, and self-supervised methods. The paper also discusses the role of DL in optimizing acquisition protocols, enhancing robustness against distribution shifts, and tackling subtle bias. Drawing on the extensive literature and practical insights, it outlines current successes, limitations, and future directions for leveraging DL in MRI reconstruction, while emphasizing the potential of DL to significantly impact clinical imaging practices.

Deep Learning for Accelerated and Robust MRI Reconstruction: a Review

Introduction

The paper provides an extensive review of the integration of Deep Learning (DL) technologies in the enhancement of Magnetic Resonance Imaging (MRI) reconstruction processes. MRI stands as a crucial diagnostic tool, but its utility is often limited by the inherent compromises between acquisition speed and image quality. The incorporation of DL offers a pathway to mitigate such limitations, leveraging advancements from both parallel imaging (PI) and compressed sensing (CS) frameworks to the field of neural network-based methods.

Historical Context and Traditional Methods

The review outlines the evolution of MRI reconstruction techniques. Traditional high-resolution imaging demanded prolonged scan times, exacerbating patient discomfort and increasing motion artifacts risks. The introduction of PI and CS techniques marked significant improvements by enabling image reconstruction from sub-Nyquist sampled data thus reducing scan times. However, these techniques often required specific acquisition schemes and were computationally intensive.

Deep Learning Advancements

Recent years have seen transformative impacts of DL in MRI reconstruction, primarily through neural networks trained end-to-end for learning the translation from undersampled and/or noisy MRI data to high-quality images. Among the neural network architectures employed, CNNs and more recently, transformer models, have shown promise. Furthermore, unrolled network architectures inspired by iterative optimization methods used in CS have led to the development of hybrid models that iteratively refine reconstruction quality.

Unrolled Network Techniques

Unrolled networks symbolize a significant merger between traditional optimization-based imaging methods and deep learning. By alternating between learned data consistency layers and learned regularization layers (often implemented via CNNs), these networks mimic iterative optimization schemes but with dramatically improved speed due to the learning process which approximates the iterative steps.

Generative Models and Self-Supervised Learning

The paper also highlights the incorporation of generative models like GANs and the emergent diffusion models which have demonstrated capabilities in reconstructing MRI images from severely undersampled data. On the other hand, self-supervised learning methods, which do not rely on fully sampled reference data, present a formidable option for training reconstruction networks directly from undersampled data without explicit ground-truth.

Future Directions and Challenges

Although DL methods have significantly pushed the frontiers of MRI reconstruction, the paper suggests that future research should focus on enhancing the robustness and stability of these methods. This involves addressing susceptibility to distribution shifts and refining acquisition protocols to not only improve the quality of reconstruction but also to tailor them towards specific clinical needs.

Uncertainty and Robustness in Deep Learning Methods

Another critical focus is on developing methods to effectively quantify and utilize uncertainty in DL-based reconstructions. This aspect is crucial for translating these technologies from research prototypes to clinical use, where trust in algorithmic decisions is paramount. Enhancing model generalization across diverse clinical settings remains an ongoing challenge.

Conclusion

The review underscores DL's profound impact on MRI reconstruction, offering methods that significantly speed up the imaging process while improving image quality. Moving forward, the integration of robustness and uncertainty assessments in DL models will be crucial for their adoption in routine clinical practices. The continuous evolution of DL techniques holds the potential to redefine the capabilities of MRI technology in medical diagnostics.

Definition Search Book Streamline Icon: https://streamlinehq.com
References (322)
  1. G. Constantine, K. Shan, S. D. Flamm, and M. U. Sivananthan, “Role of MRI in clinical cardiology,” The Lancet, vol. 363, no. 9427, pp. 2162–2171, 2004.
  2. M. Zaitsev, J. Maclaren, and M. Herbst, “Motion artifacts in MRI: A complex problem with many partial solutions,” Journal of Magnetic Resonance Imaging, vol. 42, pp. 887–901, 10 2015.
  3. D. K. Sodickson and W. J. Manning, “Simultaneous acquisition of spatial harmonics (SMASH): Fast imaging with radiofrequency coil arrays,” Magnetic Resonance in Medicine, vol. 38, 1997.
  4. M. A. Griswold et al., “Generalized autocalibrating partially parallel acquisitions (GRAPPA),” Magnetic Resonance in Medicine, vol. 47, no. 6, pp. 1202–1210, 2002.
  5. K. P. Pruessmann, M. Weiger, M. B. Scheidegger, and P. Boesiger, “SENSE: Sensitivity encoding for fast MRI,” Magnetic Resonance in Medicine, vol. 42, no. 5, pp. 952–962, 1999.
  6. N. Seiberlich, F. A. Breuer, M. Blaimer, K. Barkauskas, P. M. Jakob, and M. A. Griswold, “Non-Cartesian data reconstruction using GRAPPA operator gridding (GROG),” Magnetic Resonance in Medicine, vol. 58, pp. 1257–1265, 12 2007.
  7. A. Deshmane, V. Gulani, M. Griswold, and N. Seiberlich, “Parallel MR imaging,” Journal of Magnetic Resonance Imaging, vol. 36, no. 1, pp. 55–72, 2012.
  8. M. Lustig and J. M. Pauly, “SPIRiT: iterative self-consistent parallel imaging reconstruction from arbitrary k-space,” Magn. Reson. Med., vol. 64, no. 2, pp. 457–471, 2010.
  9. M. Lustig, D. Donoho, and J. M. Pauly, “Sparse MRI: The application of compressed sensing for rapid MR imaging,” Magnetic Resonance in Medicine, vol. 58, no. 6, pp. 1182–1195, 2007.
  10. D. L. Donoho, “Compressed Sensing,” IEEE Transactions on information theory, vol. 52, no. 4, pp. 1289–1306, 2006.
  11. H. Jung, K. Sung, K. S. Nayak, E. Y. Kim, and J. C. Ye, “k-t FOCUSS: a general compressed sensing framework for high resolution dynamic MRI,” Magnetic Resonance in Medicine, vol. 61, no. 1, pp. 103–116, 2009.
  12. L. Feng, L. Axel, H. Chandarana, K. T. Block, D. K. Sodickson, and R. Otazo, “XD-GRASP: golden-angle radial MRI with reconstruction of extra motion-state dimensions using compressed sensing,” Magnetic Resonance in Medicine, vol. 75, no. 2, pp. 775–788, 2016.
  13. M. F. Duarte and Y. C. Eldar, “Structured compressed sensing: From theory to applications,” IEEE Transactions on Signal Processing, vol. 59, pp. 4053–4085, 9 2011.
  14. J. C. Ye, “Compressed sensing MRI: a review from signal processing perspective,” BMC Biomedical Engineering, vol. 1, no. 1, pp. 1–17, 2019.
  15. S. G. Lingala and M. Jacob, “Blind compressive sensing dynamic MRI,” IEEE transactions on medical imaging, vol. 32, no. 6, pp. 1132–1145, 2013.
  16. J. A. Fessler, “Optimization methods for magnetic resonance image reconstruction: Key models and optimization algorithms,” IEEE signal processing magazine, vol. 37, no. 1, pp. 33–40, 2020.
  17. Y. LeCun, Y. Bengio, and G. Hinton, “Deep learning,” nature, vol. 521, no. 7553, pp. 436–444, 2015.
  18. L. Alzubaidi, J. Zhang, A. J. Humaidi, A. Al-Dujaili, Y. Duan, O. Al-Shamma, J. Santamaría, M. A. Fadhel, M. Al-Amidie, and L. Farhan, “Review of deep learning: Concepts, CNN architectures, challenges, applications, future directions,” Journal of big Data, vol. 8, pp. 1–74, 2021.
  19. A. Shrestha and A. Mahmood, “Review of deep learning algorithms and architectures,” IEEE access, vol. 7, pp. 53 040–53 065, 2019.
  20. S. S. Chandra, M. Bran Lorenzana, X. Liu, S. Liu, S. Bollmann, and S. Crozier, “Deep learning in magnetic resonance image reconstruction,” Journal of Medical Imaging and Radiation Oncology, vol. 65, no. 5, pp. 564–577, 2021.
  21. B. Zhu, J. Z. Liu, S. F. Cauley, B. R. Rosen, and M. S. Rosen, “Image reconstruction by domain-transform manifold learning,” Nature, vol. 555, no. 7697, pp. 487–492, 2018.
  22. S. Wang, H. Cheng, L. Ying, T. Xiao, Z. Ke, H. Zheng, and D. Liang, “DeepcomplexMRI: Exploiting deep residual network for fast parallel MR imaging with complex convolution,” Magnetic Resonance Imaging, vol. 68, pp. 136–147, 5 2020.
  23. K. Hammernik et al., “Learning a variational network for reconstruction of accelerated MRI data,” Magnetic Resonance in Medicine, vol. 79, no. 6, pp. 3055–3071, 2018.
  24. H. K. Aggarwal, M. P. Mani, and M. Jacob, “MoDL: Model-based deep learning architecture for inverse problems,” IEEE transactions on medical imaging, vol. 38, no. 2, pp. 394–405, 2018.
  25. A. S. Lundervold and A. Lundervold, “An overview of deep learning in medical imaging focusing on MRI,” Zeitschrift für Medizinische Physik, vol. 29, no. 2, pp. 102–127, 2019.
  26. M. A. Mazurowski, M. Buda, A. Saha, and M. R. Bashir, “Deep learning in radiology: An overview of the concepts and a survey of the state of the art with focus on MRI,” Journal of magnetic resonance imaging, vol. 49, no. 4, pp. 939–954, 2019.
  27. S. Ravishankar, J. C. Ye, and J. A. Fessler, “Image reconstruction: From sparsity to data-adaptive methods and machine learning,” Proceedings of the IEEE, vol. 108, no. 1, pp. 86–109, 2019.
  28. F. Knoll, K. Hammernik, C. Zhang, S. Moeller, T. Pock, D. K. Sodickson, and M. Akcakaya, “Deep-learning methods for parallel magnetic resonance imaging reconstruction: A survey of the current approaches, trends, and issues,” IEEE signal processing magazine, vol. 37, no. 1, pp. 128–140, 2020.
  29. D. Liang, J. Cheng, Z. Ke, and L. Ying, “Deep magnetic resonance image reconstruction: Inverse problems meet neural networks,” IEEE Signal Processing Magazine, vol. 37, no. 1, pp. 141–151, 2020.
  30. F. Knoll et al., “fastMRI: A publicly available raw k-space and DICOM dataset of knee images for accelerated MR image reconstruction using machine learning,” Radiology: Artificial Intelligence, vol. 2, no. 1, 2020.
  31. F. Ong, S. Amin, S. Vasanawala, and M. Lustig, “Mridata.org: An open archive for sharing MRI raw data,” in Proc. Intl. Soc. Mag. Reson. Med, vol. 26, 2018, p. 1.
  32. R. Souza, O. Lucena, J. Garrafa, D. Gobbi, M. Saluzzi, S. Appenzeller, L. Rittner, R. Frayne, and R. Lotufo, “An open, multi-vendor, multi-field-strength brain MR dataset and analysis of publicly available skull stripping methods agreement,” NeuroImage, vol. 170, pp. 482–494, 2018.
  33. A. D. Desai et al., “SKM-TEA: A Dataset for Accelerated MRI Reconstruction with Dense Image Labels for Quantitative Clinical Evaluation,” in Thirty-fifth Conference on Neural Information Processing Systems Datasets and Benchmarks Track, 2021.
  34. M. J. Muckley, B. Riemenschneider, A. Radmanesh, S. Kim, G. Jeong, J. Ko, Y. Jun, H. Shin, D. Hwang, M. Mostapha et al., “Results of the 2020 fastMRI challenge for machine learning MR image reconstruction,” IEEE transactions on medical imaging, vol. 40, no. 9, pp. 2306–2317, 2021.
  35. F. Knoll, T. Murrell, A. Sriram, N. Yakubova, J. Zbontar, M. Rabbat, A. Defazio, M. J. Muckley, D. K. Sodickson, C. L. Zitnick et al., “Advancing machine learning for MR image reconstruction with an open competition: Overview of the 2019 fastMRI challenge,” Magnetic resonance in medicine, vol. 84, no. 6, pp. 3054–3070, 2020.
  36. M. J. Muckley, B. Riemenschneider, A. Radmanesh, S. Kim, G. Jeong, J. Ko, Y. Jun, H. Shin, D. Hwang, M. Mostapha et al., “State-of-the-art machine learning MRI reconstruction in 2020: Results of the second fastMRI challenge,” arXiv preprint arXiv:2012.06318, vol. 2, no. 6, p. 7, 2020.
  37. A. A. Tolpadi, U. Bharadwaj, K. T. Gao, R. Bhattacharjee, F. G. Gassert, J. Luitjens, P. Giesler, J. N. Morshuis, P. Fischer, M. Hein et al., “K2S Challenge: From Undersampled K-Space to Automatic Segmentation,” Bioengineering, vol. 10, no. 2, p. 267, 2023.
  38. Pal, Arghya and Rathi, Yogesh, “A review and experimental evaluation of deep learning methods for MRI reconstruction,” The journal of machine learning for biomedical imaging, vol. 1, 2022.
  39. D. J. Lin, P. M. Johnson, F. Knoll, and Y. W. Lui, “Artificial intelligence for MR image reconstruction: an overview for clinicians,” Journal of Magnetic Resonance Imaging, vol. 53, no. 4, pp. 1015–1028, 2021.
  40. J. A. Oscanoa, M. J. Middione, C. Alkan, M. Yurt, M. Loecher, S. S. Vasanawala, and D. B. Ennis, “Deep Learning-Based Reconstruction for Cardiac MRI: A Review,” Bioengineering 2023, Vol. 10, Page 334, vol. 10, p. 334, 3 2023.
  41. V. Spieker, H. Eichhorn, K. Hammernik, D. Rueckert, C. Preibisch, D. C. Karampinos, and J. A. Schnabel, “Deep Learning for Retrospective Motion Correction in MRI: A Comprehensive Review,” IEEE Transactions on Medical Imaging, 5 2023.
  42. K. Hammernik, T. Klatzer, E. Kobler, M. P. Recht, D. K. Sodickson, T. Pock, and F. Knoll, “Learning a variational network for reconstruction of accelerated MRI data,” Magnetic resonance in medicine, vol. 79, no. 6, pp. 3055–3071, 2018.
  43. B. Bilgic, V. K. Goyal, and E. Adalsteinsson, “Multi-contrast reconstruction with Bayesian compressed sensing,” Magnetic resonance in medicine, vol. 66, no. 6, pp. 1601–1615, 2011.
  44. K. Hammernik, J. Schlemper, C. Qin, J. Duan, R. M. Summers, and D. Rueckert, “Systematic evaluation of iterative deep neural networks for fast parallel MRI reconstruction with sensitivity-weighted coil combination,” Magnetic Resonance in Medicine, vol. 86, no. 4, pp. 1859–1872, 2021.
  45. G. Luo, N. Zhao, W. Jiang, E. S. Hui, and P. Cao, “MRI reconstruction using deep Bayesian estimation,” Magnetic resonance in medicine, vol. 84, no. 4, pp. 2246–2261, 2020.
  46. S. Boyd, N. Parikh, E. Chu, B. Peleato, J. Eckstein et al., “Distributed optimization and statistical learning via the alternating direction method of multipliers,” Foundations and Trends® in Machine learning, vol. 3, no. 1, pp. 1–122, 2011.
  47. A. Beck and M. Teboulle, “A fast iterative shrinkage-thresholding algorithm for linear inverse problems,” SIAM journal on imaging sciences, vol. 2, no. 1, pp. 183–202, 2009.
  48. M. J. Muckley, B. Riemenschneider, A. Radmanesh, S. Kim, G. Jeong, J. Ko, Y. Jun, H. Shin, D. Hwang, M. Mostapha et al., “Results of the 2020 fastMRI challenge for machine learning MR image reconstruction,” IEEE transactions on medical imaging, vol. 40, pp. 2306–2317, 2021.
  49. S. Wang et al., “Accelerating magnetic resonance imaging via deep learning,” 2016, pp. 514–517.
  50. K. H. Jin, M. T. McCann, E. Froustey, and M. Unser, “Deep convolutional neural network for inverse problems in imaging,” IEEE transactions on image processing, vol. 26, no. 9, pp. 4509–4522, 2017.
  51. K. Lin and R. Heckel, “Vision Transformers Enable Fast and Robust Accelerated MRI,” pp. 774–795, 12 2022. [Online]. Available: https://proceedings.mlr.press/v172/lin22a.html
  52. ——, “Vision transformers enable fast and robust accelerated MRI,” in International Conference on Medical Imaging with Deep Learning.    PMLR, 2022, pp. 774–795.
  53. P. Guo, Y. Mei, J. Zhou, S. Jiang, and V. M. Patel, “ReconFormer: Accelerated MRI reconstruction using recurrent transformer,” IEEE transactions on medical imaging, 2023.
  54. K. Gregor and Y. LeCun, “Learning Fast Approximations of Sparse Coding,” in Proceedings of the 27th International Conference on International Conference on Machine Learning, ser. ICML’10.    USA: Omnipress, 2010, pp. 399–406.
  55. J. Sun, H. Li, Z. Xu et al., “Deep admm-net for compressive sensing mri,” Advances in neural information processing systems, vol. 29, 2016.
  56. J. Schlemper, J. Caballero, J. V. Hajnal, A. N. Price, and D. Rueckert, “A Deep Cascade of Convolutional Neural Networks for Dynamic MR Image Reconstruction,” IEEE Transactions on Medical Imaging, vol. 37, pp. 491–503, 2 2018.
  57. A. Sriram, J. Zbontar, T. Murrell, A. Defazio, C. L. Zitnick, N. Yakubova, F. Knoll, and P. Johnson, “End-to-End Variational Networks for Accelerated MRI Reconstruction,” arXiv:2004.06688, 2020.
  58. Z. Fabian, B. Tinaz, and M. Soltanolkotabi, “HUMUS-Net: Hybrid Unrolled Multi-scale Network Architecture for Accelerated MRI Reconstruction,” Advances in Neural Information Processing Systems, vol. 35, pp. 25 306–25 319, 2022.
  59. M. Z. Darestani, V. Nath, W. Li, Y. He, H. R. Roth, Z. Xu, D. Xu, R. Heckel, and C. Zhao, “IR-FRestormer: Iterative Refinement With Fourier-Based Restormer for Accelerated MRI Reconstruction,” in Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision, 2024, pp. 7655–7664.
  60. A. Pramanik, H. K. Aggarwal, and M. Jacob, “Deep generalization of structured low-rank algorithms (Deep-SLR),” IEEE transactions on medical imaging, vol. 39, no. 12, pp. 4186–4197, 2020.
  61. T. Eo, Y. Jun, T. Kim, J. Jang, H.-J. Lee, and D. Hwang, “KIKI-net: cross-domain convolutional neural networks for reconstructing undersampled magnetic resonance images,” Magnetic resonance in medicine, vol. 80, no. 5, pp. 2188–2201, 2018.
  62. B. Wang, Y. Lian, X. Xiong, H. Zhou, Z. Liu, and X. Zhou, “DCT-net: Dual-domain cross-fusion transformer network for MRI reconstruction,” Magnetic Resonance Imaging, 2024.
  63. D. Gilton, G. Ongie, and R. Willett, “Deep equilibrium architectures for inverse problems in imaging,” IEEE Transactions on Computational Imaging, vol. 7, pp. 1123–1133, 2021.
  64. A. Pramanik, M. B. Zimmerman, and M. Jacob, “Memory-efficient model-based deep learning with convergence and robustness guarantees,” IEEE Transactions on Computational Imaging, vol. 9, pp. 260–275, 2023.
  65. A. Pramanik and M. Jacob, “Accelerated parallel MRI using memory efficient and robust monotone operator learning (MOL),” in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI).    IEEE, 2023, pp. 1–4.
  66. K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, “Image denoising by sparse 3-D transform-domain collaborative filtering,” vol. 16, no. 8, pp. 2080–2095, 2007.
  67. R. Ahmad, C. A. Bouman, G. T. Buzzard, S. Chan, S. Liu, E. T. Reehorst, and P. Schniter, “Plug-and-Play Methods for Magnetic Resonance Imaging: Using Denoisers for Image Recovery,” vol. 37, no. 1, pp. 105–116, 2020.
  68. U. S. Kamilov, C. A. Bouman, G. T. Buzzard, and B. Wohlberg, “Plug-and-Play Methods for Integrating Physical and Learned Models in Computational Imaging,” arXiv:2203.17061 [eess], 2022.
  69. E. Ryu, J. Liu, S. Wang, X. Chen, Z. Wang, and W. Yin, “Plug-and-play methods provably converge with properly trained denoisers,” in International Conference on Machine Learning.    PMLR, 2019, pp. 5546–5557.
  70. D. P. Kingma and M. Welling, “Auto-encoding variational bayes,” arXiv preprint arXiv:1312.6114, 2013.
  71. K. C. Tezcan, C. F. Baumgartner, R. Luechinger, K. P. Pruessmann, and E. Konukoglu, “MR image reconstruction using deep density priors,” IEEE transactions on medical imaging, vol. 38, no. 7, pp. 1633–1642, 2018.
  72. I. J. Goodfellow, J. Pouget-Abadie, M. Mirza, B. Xu, D. Warde-Farley, S. Ozair, A. Courville, and Y. Bengio, “Generative adversarial networks,” arXiv preprint arXiv:1406.2661, 2014.
  73. G. Yang, S. Yu, H. Dong, G. Slabaugh, P. L. Dragotti, X. Ye, F. Liu, S. Arridge, J. Keegan, Y. Guo et al., “DAGAN: Deep de-aliasing generative adversarial networks for fast compressed sensing MRI reconstruction,” IEEE transactions on medical imaging, vol. 37, no. 6, pp. 1310–1321, 2017.
  74. M. Mardani et al., “Deep generative adversarial neural networks for compressive sensing MRI,” IEEE Transactions on Medical Imaging, vol. 38, no. 1, pp. 167–179, 2018.
  75. T. M. Quan, T. Nguyen-Duc, and W.-K. Jeong, “Compressed sensing MRI reconstruction using a generative adversarial network with a cyclic loss,” IEEE transactions on medical imaging, vol. 37, no. 6, pp. 1488–1497, 2018.
  76. E. K. Cole, J. M. Pauly, S. S. Vasanawala, and F. Ong, “Unsupervised MRI reconstruction with generative adversarial networks,” arXiv preprint arXiv:2008.13065, 2020.
  77. J. Lv, J. Zhu, and G. Yang, “Which GAN? A comparative study of generative adversarial network-based fast MRI reconstruction,” Philosophical Transactions of the Royal Society A, vol. 379, no. 2200, p. 20200203, 2021.
  78. Y. Korkmaz, S. U. Dar, M. Yurt, M. Özbey, and T. Cukur, “Unsupervised MRI reconstruction via zero-shot learned adversarial transformers,” IEEE Transactions on Medical Imaging, 2022.
  79. L. Yang, Z. Zhang, Y. Song, S. Hong, R. Xu, Y. Zhao, W. Zhang, B. Cui, and M.-H. Yang, “Diffusion models: A comprehensive survey of methods and applications,” ACM Computing Surveys, vol. 56, no. 4, pp. 1–39, 2023.
  80. R. Po, W. Yifan, V. Golyanik, K. Aberman, J. T. Barron, A. H. Bermano, E. R. Chan, T. Dekel, A. Holynski, A. Kanazawa et al., “State of the art on diffusion models for visual computing,” arXiv preprint arXiv:2310.07204, 2023.
  81. F.-A. Croitoru, V. Hondru, R. T. Ionescu, and M. Shah, “Diffusion models in vision: A survey,” IEEE Transactions on Pattern Analysis and Machine Intelligence, 2023.
  82. B. Kawar, M. Elad, S. Ermon, and J. Song, “Denoising Diffusion Restoration Models,” in Neural Information Processing Systems (NeurIPS), 2022.
  83. A. Bora, A. Jalal, E. Price, and A. G. Dimakis, “Compressed Sensing Using Generative Models,” in International Conference on Machine Learning, 2017.
  84. M. Asim, M. Daniels, O. Leong, A. Ahmed, and P. Hand, “Invertible Generative Models for Inverse Problems: Mitigating Representation Error and Dataset Bias,” in International Confernce on Machine Learning, 2020.
  85. A. Jalal, M. Arvinte, G. Daras, E. Price, A. G. Dimakis, and J. I. Tamir, “Robust Compressed Sensing MRI with Deep Generative Priors,” 2021.
  86. G. Daras, W.-S. Chu, A. Kumar, D. Lagun, and A. G. Dimakis, “Solving Inverse Problems with NerfGANs,” arXiv:2112.09061, 2021.
  87. A. Güngör, S. U. Dar, Ş. Öztürk, Y. Korkmaz, H. A. Bedel, G. Elmas, M. Ozbey, and T. Çukur, “Adaptive diffusion priors for accelerated MRI reconstruction,” Medical Image Analysis, p. 102872, 2023.
  88. J. Ho, A. Jain, and P. Abbeel, “Denoising diffusion probabilistic models,” Advances in neural information processing systems, vol. 33, pp. 6840–6851, 2020.
  89. H. Chung and J. C. Ye, “Score-based diffusion models for accelerated MRI,” Medical Image Analysis, p. 102479, 2022.
  90. G. Luo, M. Blumenthal, M. Heide, and M. Uecker, “Bayesian MRI reconstruction with joint uncertainty estimation using diffusion models,” Magnetic Resonance in Medicine, vol. 90, no. 1, pp. 295–311, 2023.
  91. M. Zach, F. Knoll, and T. Pock, “Stable deep MRI reconstruction using Generative Priors,” IEEE Transactions on Medical Imaging, 2023.
  92. H. Ali, M. R. Biswas, F. Mohsen, U. Shah, A. Alamgir, O. Mousa, and Z. Shah, “The role of generative adversarial networks in brain MRI: a scoping review,” Insights into imaging, vol. 13, no. 1, p. 98, 2022.
  93. Y. Song and S. Ermon, “Improved Techniques for Training Score-Based Generative Models,” in Advances in Neural Information Processing Systems, 2020.
  94. Y. Song, J. Sohl-Dickstein, D. P. Kingma, A. Kumar, S. Ermon, and B. Poole, “Score-based generative modeling through stochastic differential equations,” arXiv preprint arXiv:2011.13456, 2020.
  95. H. Chung, J. Kim, M. T. Mccann, M. L. Klasky, and J. C. Ye, “Diffusion posterior sampling for general noisy inverse problems,” arXiv preprint arXiv:2209.14687, 2022.
  96. C. Yu, Y. Guan, Z. Ke, K. Lei, D. Liang, and Q. Liu, “Universal generative modeling in dual domains for dynamic MRI,” NMR in Biomedicine, vol. 36, no. 12, p. e5011, 2023.
  97. A. Jalal, M. Arvinte, G. Daras, E. Price, A. G. Dimakis, and J. Tamir, “Robust compressed sensing MRI with deep generative priors,” Advances in Neural Information Processing Systems, vol. 34, pp. 14 938–14 954, 2021.
  98. B. Levac, A. Jalal, and J. I. Tamir, “Accelerated Motion Correction for MRI Using Score-Based Generative Models,” in IEEE International Symposium on Biomedical Imaging (ISBI), 2023, pp. 1–5.
  99. C. Alkan, J. Oscanoa, D. Abraham, M. Gao, A. Nurdinova, K. Setsompop, J. M. Pauly, M. Mardani, and S. Vasanawala, “Variational Diffusion Models for Blind MRI Inverse Problems,” in NeurIPS 2023 Workshop on Deep Learning and Inverse Problems, 2023.
  100. B. Levac, A. Jalal, K. Ramchandran, and J. Tamir, “MRI reconstruction with side information using diffusion models,” arXiv preprint arXiv:2303.14795, 2023.
  101. D. Ulyanov, A. Vedaldi, and V. Lempitsky, “Deep Image Prior,” International Journal of Computer Vision, 2020.
  102. D. P. Kingma and J. L. Ba, “Adam: a Method for Stochastic Optimization,” International Conference on Learning Representations 2015, pp. 1–15, 2015.
  103. R. Heckel and M. Soltanolkotabi, “Denoising and Regularization via Exploiting the Structural Bias of Convolutional Generators,” in International Conference on Learning Representations, 2020.
  104. R. Heckel and P. Hand, “Deep Decoder: Concise Image Representations from Untrained Non-convolutional Networks,” in International Conference on Learning Representations, 2019.
  105. R. Heckel and M. Soltanolkotabi, “Compressive Sensing with Un-Trained Neural Networks: Gradient Descent Finds the Smoothest Approximation,” in International Conference on Machine Learning, 2020.
  106. M. Z. Darestani and R. Heckel, “Accelerated MRI with un-trained neural networks,” IEEE Transactions on Computational Imaging, vol. 7, p. 724–733, 2021.
  107. K. H. Jin, H. Gupta, J. Yerly, M. Stuber, and M. Unser, “Time-Dependent Deep Image Prior for Dynamic MRI,” arXiv:1910.01684, 2019.
  108. Q. Zou, A. H. Ahmed, P. Nagpal, S. Kruger, and M. Jacob, “Dynamic imaging using a deep generative storm (gen-storm) model,” IEEE Transactions on Medical Imaging, 2021.
  109. A. H. Ahmed, R. Zhou, Y. Yang, P. Nagpal, M. Salerno, and M. Jacob, “Free-breathing and ungated dynamic mri using navigator-less spiral storm,” IEEE Transactions on Medical Imaging, vol. 39, no. 12, pp. 3933–3943, 2020.
  110. S. Poddar, Y. Q. Mohsin, D. Ansah, B. Thattaliyath, R. Ashwath, and M. Jacob, “Manifold recovery using kernel low-rank regularization: Application to dynamic imaging,” IEEE Transactions on Computational Imaging, vol. 5, no. 3, pp. 478–491, 2019.
  111. B. Mildenhall, P. P. Srinivasan, M. Tancik, J. T. Barron, R. Ramamoorthi, and R. Ng, “Nerf: Representing scenes as neural radiance fields for view synthesis,” Communications of the ACM, vol. 65, no. 1, pp. 99–106, 2021.
  112. R. Arandjelović and A. Zisserman, “NeRF in Detail: Learning to Sample for View Synthesis,” arXiv:2106.05264, 2021.
  113. F. Williams, T. Schneider, C. Silva, D. Zorin, J. Bruna, and D. Panozzo, “Deep Geometric Prior for Surface Reconstruction,” in Conference on Computer Vision and Pattern Recognition, 2019.
  114. W. Huang, H. B. Li, J. Pan, G. Cruz, D. Rueckert, and K. Hammernik, “Neural Implicit k-Space for Binning-Free Non-Cartesian Cardiac MR Imaging,” in International Conference on Information Processing in Medical Imaging.    Springer, 2023, pp. 548–560.
  115. M. Tancik, P. Srinivasan, B. Mildenhall, S. Fridovich-Keil, N. Raghavan, U. Singhal, R. Ramamoorthi, J. Barron, and R. Ng, “Fourier features let networks learn high frequency functions in low dimensional domains,” Advances in Neural Information Processing Systems, vol. 33, pp. 7537–7547, 2020.
  116. E. Dupont, A. Goliński, M. Alizadeh, Y. W. Teh, and A. Doucet, “COIN: COmpression with Implicit Neural Representations,” arXiv:2103.03123 [cs, eess], 2021.
  117. V. Sitzmann, J. N. P. Martel, A. W. Bergman, D. B. Lindell, and G. Wetzstein, “Implicit Neural Representations with Periodic Activation Functions,” arXiv:2006.09661 [cs, eess], 2020.
  118. W. Huang, H. Li, G. Cruz, J. Pan, D. Rueckert, and K. Hammernik, “Neural Implicit K-Space for Binning-free Non-Cartesian Cardiac MR Imaging,” 2022.
  119. J. F. Kunz, S. Ruschke, and R. Heckel, “Implicit Neural Networks with Fourier-Feature Inputs for Free-breathing Cardiac MRI Reconstruction,” 2023.
  120. B. Yaman, S. A. H. Hosseini, S. Moeller, J. Ellermann, K. Ugurbil, and M. Akcakaya, “Self-supervised physics-based deep learning MRI reconstruction without fully-sampled data,” 2020, pp. 921–925.
  121. C. Millard and M. Chiew, “Simultaneous self-supervised reconstruction and denoising of sub-sampled MRI data with Noisier2Noise,” arXiv preprint arXiv:2210.01696, 2022.
  122. Y. Chen, J. H. Holmes, C. Corum, V. Magnotta, and M. Jacob, “Deep Factor Model: A Novel Approach for Motion Compensated Multi-Dimensional MRI,” in IEEE international Symposium on Biomedical Imaging, 2023.
  123. F. Wang, H. Qi, A. De Goyeneche, R. Heckel, M. Lustig, and E. Shimron, “K-band: Self-supervised mri reconstruction via stochastic gradient descent over k-space subsets,” arXiv preprint arXiv:2308.02958, 2023.
  124. M. Akçakaya, B. Yaman, H. Chung, and J. C. Ye, “Unsupervised Deep Learning Methods for Biological Image Reconstruction and Enhancement: An overview from a signal processing perspective,” IEEE Signal Processing Magazine, vol. 39, no. 2, pp. 28–44, 2022.
  125. G. Zeng, Y. Guo, J. Zhan, Z. Wang, Z. Lai, X. Du, X. Qu, and D. Guo, “A review on deep learning MRI reconstruction without fully sampled k-space,” BMC Medical Imaging, vol. 21, no. 1, p. 195, 2021.
  126. C. M. Stein, “Estimation Of The Mean Of A Multivariate Normal Distribution,” The annals of Statistics, pp. 1135–1151, 1981.
  127. S. Ramani, T. Blu, and M. Unser, “Monte-Carlo SURE: A Black-Box Optimization Of Regularization Parameters For General Denoising Algorithms,” vol. 17, no. 9, pp. 1540–1554, 2008.
  128. C. A. Metzler, A. Mousavi, R. Heckel, and R. G. Baraniuk, “Unsupervised Learning with Stein’s Unbiased Risk Estimator,” arXiv preprint arXiv:1805.10531, 2018.
  129. M. Zhussip, S. Soltanayev, and S. Y. Chun, “Training deep learning based image denoisers from undersampled measurements without ground truth and without image prior,” in IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2019, pp. 10 255–10 264.
  130. Y. C. Eldar, “Generalized SURE for Exponential Families: Applications to Regularization,” vol. 57, no. 2, pp. 471–481, 2008.
  131. D. L. Donoho and I. M. Johnstone, “Adapting To Unknown Smoothness Via Wavelet Shrinkage,” Journal of the American Statistical Association, vol. 90, no. 432, pp. 1200–1224, 1995.
  132. J. Lehtinen, J. Munkberg, J. Hasselgren, S. Laine, T. Karras, M. Aittala, and T. Aila, “Noise2Noise: Learning Image Restoration without Clean Data,” in International Conference on Machine Learning, 2018, pp. 2971–2980.
  133. T. Klug, D. Atik, and R. Heckel, “Analyzing the Sample Complexity of Self-Supervised Image Reconstruction Methods,” in Neural Information Processing Systems (NeurIPS).    arXiv, 2023.
  134. C. Millard and M. Chiew, “A theoretical framework for self-supervised MR image reconstruction using sub-sampling via variable density Noisier2Noise,” IEEE transactions on computational imaging, 2023.
  135. N. Moran, D. Schmidt, Y. Zhong, and P. Coady, “Noisier2noise: Learning to denoise from unpaired noisy data,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2020, pp. 12 064–12 072.
  136. F. Wang, H. Qi, A. D. Goyeneche, M. Lustig, and E. Shimron, “K-band: Training self-supervised reconstruction networks using limited-resolution data,” 2023.
  137. K. Han, Y. Wang, H. Chen, X. Chen, J. Guo, Z. Liu, Y. Tang, A. Xiao, C. Xu, Y. Xu et al., “A survey on vision transformer,” IEEE transactions on pattern analysis and machine intelligence, vol. 45, no. 1, pp. 87–110, 2022.
  138. K. Han, A. Xiao, E. Wu, J. Guo, C. Xu, and Y. Wang, “Transformer in transformer,” Advances in Neural Information Processing Systems, vol. 34, pp. 15 908–15 919, 2021.
  139. A. Vaswani, N. Shazeer, N. Parmar, J. Uszkoreit, L. Jones, A. N. Gomez, Ł. Kaiser, and I. Polosukhin, “Attention is all you need,” Advances in neural information processing systems, vol. 30, 2017.
  140. A. Gillioz, J. Casas, E. Mugellini, and O. Abou Khaled, “Overview of the Transformer-based Models for NLP Tasks,” in 2020 15th Conference on Computer Science and Information Systems (FedCSIS).    IEEE, 2020, pp. 179–183.
  141. T. Wolf, L. Debut, V. Sanh, J. Chaumond, C. Delangue, A. Moi, P. Cistac, T. Rault, R. Louf, M. Funtowicz et al., “Huggingface’s transformers: State-of-the-art natural language processing,” arXiv preprint arXiv:1910.03771, 2019.
  142. Y. Korkmaz, M. Yurt, S. U. H. Dar, M. Özbey, and T. Cukur, “Deep MRI Reconstruction with Generative Vision Transformers,” Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12964 LNCS, pp. 54–64, 2021.
  143. C.-M. Feng, Y. Yan, H. Fu, L. Chen, and Y. Xu, “Task transformer network for joint MRI reconstruction and super-resolution,” in Medical Image Computing and Computer Assisted Intervention–MICCAI 2021: 24th International Conference, Strasbourg, France, September 27–October 1, 2021, Proceedings, Part VI 24.    Springer, 2021, pp. 307–317.
  144. R. Souza, M. Bento, N. Nogovitsyn, K. J. Chung, W. Loos, R. M. Lebel, and R. Frayne, “Dual-domain cascade of U-nets for multi-channel magnetic resonance image reconstruction,” Magnetic resonance imaging, vol. 71, pp. 140–153, 2020.
  145. S. Wang, Z. Ke, H. Cheng, S. Jia, L. Ying, H. Zheng, and D. Liang, “DIMENSION: dynamic MR imaging with both k-space and spatial prior knowledge obtained via multi-supervised network training,” NMR in Biomedicine, vol. 35, no. 4, p. e4131, 2022.
  146. M. Ran, W. Xia, Y. Huang, Z. Lu, P. Bao, Y. Liu, H. Sun, J. Zhou, and Y. Zhang, “Md-recon-net: A parallel dual-domain convolutional neural network for compressed sensing mri,” IEEE Transactions on Radiation and Plasma Medical Sciences, vol. 5, no. 1, pp. 120–135, 2020.
  147. N. M. Singh, J. E. Iglesias, E. Adalsteinsson, A. V. Dalca, and P. Golland, “Joint frequency and image space learning for MRI reconstruction and analysis,” The journal of machine learning for biomedical imaging, vol. 2022, 2022.
  148. X. Zhao, T. Yang, B. Li, and X. Zhang, “SwinGAN: A dual-domain Swin Transformer-based generative adversarial network for MRI reconstruction,” Computers in Biology and Medicine, vol. 153, p. 106513, 2023.
  149. Y. Gao and S. J. Reeves, “Optimal k-space sampling in MRSI for images with a limited region of support,” vol. 19, no. 12, pp. 1168–1178, 2000.
  150. D. Xu, M. Jacob, and Z. Liang, “Optimal sampling of k-space with Cartesian grids for parallel MR imaging,” in Proc. Int. Soc. Magn. Reson. Med., vol. 13, 2005, p. 2450.
  151. J. P. Haldar and D. Kim, “OEDIPUS: An experiment design framework for sparsity-constrained MRI,” 2019.
  152. E. Levine and B. Hargreaves, “On-the-fly adaptive k-space sampling for linear MRI reconstruction using moment-based spectral analysis,” vol. 37, no. 2, pp. 557–567, 2017.
  153. L. K. Senel, T. Kilic, A. Gungor, E. Kopanoglu, H. E. Guven, E. U. Saritas, A. Koc, and T. Çukur, “Statistically Segregated k-Space Sampling for Accelerating Multiple-Acquisition MRI,” vol. 38, no. 7, pp. 1701–1714, 2019.
  154. F. Sherry, M. Benning, J. C. D. l. Reyes, M. J. Graves, G. Maierhofer, G. Williams, C.-B. Schönlieb, and M. J. Ehrhardt, “Learning the sampling pattern for MRI,” arXiv preprint arXiv:1906.08754, 2019.
  155. B. Gözcü, R. K. Mahabadi, Y.-H. Li, E. Ilıcak, T. Çukur, J. Scarlett, and V. Cevher, “Learning-based compressive MRI,” vol. 37, no. 6, pp. 1394–1406, 2018.
  156. C. Lazarus, P. Weiss, N. Chauffert, F. Mauconduit, L. El Gueddari, C. Destrieux, I. Zemmoura, A. Vignaud, and P. Ciuciu, “SPARKLING: Variable-density k-space filling curves for accelerated T2*-weighted MRI,” Magn. Reson. Med., vol. 81, no. 6, pp. 3643–3661, 2019.
  157. S. Ravula, B. Levac, A. Jalal, J. I. Tamir, and A. G. Dimakis, “Optimizing Sampling Patterns for Compressed Sensing MRI with Diffusion Generative Models,” 6 2023.
  158. T. Weiss, O. Senouf, S. Vedula, O. Michailovich, M. Zibulevsky, and A. Bronstein, “PILOT: Physics-Informed Learned Optimized Trajectories for Accelerated MRI,” Machine Learning for Biomedical Imaging, vol. 1, pp. 1–23, 9 2019.
  159. C. D. Bahadir, A. Q. Wang, A. V. Dalca, and M. R. Sabuncu, “Deep-learning-based optimization of the under-sampling pattern in MRI,” IEEE Transactions on Computational Imaging, vol. 6, pp. 1139–1152, 2020.
  160. G. R. Chaithya, Z. Ramzi, and P. Ciuciu, “Learning the sampling density in 2D SPARKLING MRI acquisition for optimized image reconstruction,” European Signal Processing Conference, vol. 2021-August, pp. 960–964, 2021.
  161. M. V. W. Zibetti, F. Knoll, and R. R. Regatte, “Alternating learning approach for variational networks and undersampling pattern in parallel MRI applications,” IEEE Transactions on Computational Imaging, vol. 8, pp. 449–461, 2022.
  162. H. K. Aggarwal and M. Jacob, “J-modl: Joint model-based deep learning for optimized sampling and reconstruction,” IEEE Journal of Selected Topics in Signal Processing, vol. 14, no. 6, pp. 1151–1162, 2020.
  163. G. Wang, T. Luo, J. F. Nielsen, D. C. Noll, and J. A. Fessler, “B-Spline Parameterized Joint Optimization of Reconstruction and K-Space Trajectories (BJORK) for Accelerated 2D MRI,” IEEE Transactions on Medical Imaging, vol. 41, pp. 2318–2330, 9 2022.
  164. G. Wang, J.-F. Nielsen, J. A. Fessler, and D. C. Noll, “Stochastic optimization of 3D non-cartesian sampling trajectory (SNOPY),” arXiv preprint arXiv:2209.11030, 2022.
  165. C. G. Radhakrishna and P. Ciuciu, “Jointly Learning Non-Cartesian k-Space Trajectories and Reconstruction Networks for 2D and 3D MR Imaging through Projection,” Bioengineering 2023, Vol. 10, Page 158, vol. 10, p. 158, 1 2023.
  166. C. Alkan, M. Mardani, S. S. Vasanawala, and J. M. Pauly, “Learning to Sample MRI via Variational Information Maximization,” 10 2020.
  167. J. Xie, J. Zhang, Y. Zhang, and X. Ji, “PUERT: Probabilistic under-sampling and explicable reconstruction network for CS-MRI,” IEEE Journal of Selected Topics in Signal Processing, vol. 16, no. 4, pp. 737–749, 2022.
  168. J. Zou and Y. Cao, “Joint Optimization of kt Sampling Pattern and Reconstruction of DCE MRI for Pharmacokinetic Parameter Estimation,” IEEE Transactions on Medical Imaging, vol. 41, no. 11, pp. 3320–3331, 2022.
  169. B. Zhu, J. Liu, N. Koonjoo, B. R. Rosen, and M. S. Rosen, “AUTOmated pulse SEQuence generation (AUTOSEQ) using Bayesian reinforcement learning in an MRI physics simulation environment,” in Proceedings of Joint Annual Meeting ISMRM-ESMRMB, 2018.
  170. B. Zhu, J. Liu, N. Koonjoo, B. Rosen, and M. S. Rosen, “AUTOmated pulse SEQuence generation (AUTOSEQ) and neural network decoding for fast quantitative MR parameter measurement using continuous and simultaneous RF transmit and receive,” in ISMRM Annual Meeting & Exhibition, vol. 1090, 2019.
  171. P. K. Lee, L. E. Watkins, T. I. Anderson, G. Buonincontri, and B. A. Hargreaves, “Flexible and efficient optimization of quantitative sequences using automatic differentiation of Bloch simulations,” Magnetic resonance in medicine, vol. 82, no. 4, pp. 1438–1451, 2019.
  172. A. Loktyushin, K. Herz, N. Dang, F. Glang, A. Deshmane, S. Weinmüller, A. Doerfler, B. Schölkopf, K. Scheffler, and M. Zaiss, “MRzero-Automated discovery of MRI sequences using supervised learning,” Magnetic Resonance in Medicine, vol. 86, no. 2, pp. 709–724, 2021.
  173. H. N. Dang, J. Endres, S. Weinmüller, F. Glang, A. Loktyushin, K. Scheffler, A. Doerfler, M. Schmidt, A. Maier, and M. Zaiss, “MR-zero meets RARE MRI: Joint optimization of refocusing flip angles and neural networks to minimize T2-induced blurring in spin echo sequences,” Magnetic Resonance in Medicine, vol. 90, no. 4, pp. 1345–1362, 2023.
  174. O. Perlman, B. Zhu, M. Zaiss, M. S. Rosen, and C. T. Farrar, “An end-to-end AI-based framework for automated discovery of rapid CEST/MT MRI acquisition protocols and molecular parameter quantification (AutoCEST),” Magnetic Resonance in Medicine, vol. 87, no. 6, pp. 2792–2810, 2022.
  175. B. Kang, M. Singh, H. Park, and H.-Y. Heo, “Only-train-once MR fingerprinting for B0 and B1 inhomogeneity correction in quantitative magnetization-transfer contrast,” Magnetic Resonance in Medicine, vol. 90, no. 1, pp. 90–102, 2023.
  176. I. Beracha, A. Seginer, and A. Tal, “Adaptive model-based Magnetic Resonance,” Magnetic Resonance in Medicine, 2023.
  177. B. Zhao, K. Setsompop, H. Ye, S. F. Cauley, and L. L. Wald, “Maximum likelihood reconstruction for magnetic resonance fingerprinting,” IEEE transactions on medical imaging, vol. 35, no. 8, pp. 1812–1823, 2016.
  178. N. Seiberlich, V. Gulani, A. Campbell-Washburn, S. Sourbron, M. I. Doneva, F. Calamante, and H. H. Hu, “Quantitative magnetic resonance imaging,” 2020.
  179. N. Vladimirov and O. Perlman, “Molecular MRI-Based Monitoring of Cancer Immunotherapy Treatment Response,” International Journal of Molecular Sciences, vol. 24, no. 4, p. 3151, 2023.
  180. L. Feng, D. Ma, and F. Liu, “Rapid MR relaxometry using deep learning: An overview of current techniques and emerging trends,” NMR in Biomedicine, vol. 35, no. 4, p. e4416, 2022.
  181. F. Liu, L. Feng, and R. Kijowski, “MANTIS: model-augmented neural network with incoherent k-space sampling for efficient MR parameter mapping,” Magnetic resonance in medicine, vol. 82, no. 1, pp. 174–188, 2019.
  182. F. Liu, R. Kijowski, G. El Fakhri, and L. Feng, “Magnetic resonance parameter mapping using model-guided self-supervised deep learning,” Magnetic resonance in medicine, vol. 85, no. 6, pp. 3211–3226, 2021.
  183. H. Li, M. Yang, J. H. Kim, C. Zhang, R. Liu, P. Huang, D. Liang, X. Zhang, X. Li, and L. Ying, “SuperMAP: Deep ultrafast MR relaxometry with joint spatiotemporal undersampling,” Magnetic Resonance in Medicine, vol. 89, no. 1, pp. 64–76, 2023.
  184. D. Ma, V. Gulani, N. Seiberlich, K. Liu, J. L. Sunshine, J. L. Duerk, and M. A. Griswold, “Magnetic resonance fingerprinting,” Nature, vol. 495, no. 7440, pp. 187–192, 2013.
  185. J. Weigand-Whittier, M. Sedykh, K. Herz, J. Coll-Font, A. N. Foster, E. R. Gerstner, C. Nguyen, M. Zaiss, C. T. Farrar, and O. Perlman, “Accelerated and quantitative three-dimensional molecular MRI using a generative adversarial network,” Magnetic Resonance in Medicine, vol. 89, no. 5, pp. 1901–1914, 2023.
  186. A. Panda, B. B. Mehta, S. Coppo, Y. Jiang, D. Ma, N. Seiberlich, M. A. Griswold, and V. Gulani, “Magnetic resonance fingerprinting–an overview,” Current opinion in biomedical engineering, vol. 3, pp. 56–66, 2017.
  187. O. Cohen, B. Zhu, and M. S. Rosen, “MR fingerprinting deep reconstruction network (DRONE),” Magnetic resonance in medicine, vol. 80, no. 3, pp. 885–894, 2018.
  188. F. Balsiger, A. Shridhar Konar, S. Chikop, V. Chandran, O. Scheidegger, S. Geethanath, and M. Reyes, “Magnetic resonance fingerprinting reconstruction via spatiotemporal convolutional neural networks,” in Machine Learning for Medical Image Reconstruction: First International Workshop, MLMIR 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 16, 2018, Proceedings 1.    Springer, 2018, pp. 39–46.
  189. P. A. Gómez, M. Molina-Romero, C. Ulas, G. Bounincontri, J. I. Sperl, D. K. Jones, M. I. Menzel, and B. H. Menze, “Simultaneous parameter mapping, modality synthesis, and anatomical labeling of the brain with MR fingerprinting,” in Medical Image Computing and Computer-Assisted Intervention-MICCAI 2016: 19th International Conference, Athens, Greece, October 17-21, 2016, Proceedings, Part III 19.    Springer, 2016, pp. 579–586.
  190. P. A. Gómez, M. Cencini, M. Golbabaee, R. F. Schulte, C. Pirkl, I. Horvath, G. Fallo, L. Peretti, M. Tosetti, B. H. Menze et al., “Rapid three-dimensional multiparametric MRI with quantitative transient-state imaging,” Scientific reports, vol. 10, no. 1, p. 13769, 2020.
  191. O. Cohen, V. Y. Yu, K. R. Tringale, R. J. Young, O. Perlman, C. T. Farrar, and R. Otazo, “CEST MR fingerprinting (CEST-MRF) for brain tumor quantification using EPI readout and deep learning reconstruction,” Magnetic Resonance in Medicine, vol. 89, no. 1, pp. 233–249, 2023.
  192. O. Perlman, H. Ito, K. Herz, N. Shono, H. Nakashima, M. Zaiss, E. A. Chiocca, O. Cohen, M. S. Rosen, and C. T. Farrar, “Quantitative imaging of apoptosis following oncolytic virotherapy by magnetic resonance fingerprinting aided by deep learning,” Nature biomedical engineering, vol. 6, no. 5, pp. 648–657, 2022.
  193. O. Perlman, K. Herz, M. Zaiss, O. Cohen, M. S. Rosen, and C. T. Farrar, “CEST MR-fingerprinting: practical considerations and insights for acquisition schedule design and improved reconstruction,” Magnetic resonance in medicine, vol. 83, no. 2, pp. 462–478, 2020.
  194. D. Nagar, N. Vladimirov, C. T. Farrar, and O. Perlman, “Dynamic and rapid deep synthesis of chemical exchange saturation transfer and semisolid magnetization transfer MRI signals,” Scientific Reports, vol. 13, no. 1, p. 18291, 2023.
  195. M. Singh, S. Jiang, Y. Li, P. van Zijl, J. Zhou, and H.-Y. Heo, “Bloch simulator–driven deep recurrent neural network for magnetization transfer contrast MR fingerprinting and CEST imaging,” Magnetic Resonance in Medicine, 2023.
  196. I. Blystad, J. B. M. Warntjes, O. Smedby, A.-M. Landtblom, P. Lundberg, and E.-M. Larsson, “Synthetic MRI of the brain in a clinical setting,” Acta radiologica, vol. 53, no. 10, pp. 1158–1163, 2012.
  197. O. Perlman, C. T. Farrar, and H.-Y. Heo, “MR fingerprinting for semisolid magnetization transfer and chemical exchange saturation transfer quantification,” NMR in Biomedicine, vol. 36, no. 6, p. e4710, 2023.
  198. K. Wang, M. Doneva, J. Meineke, T. Amthor, E. Karasan, F. Tan, J. I. Tamir, S. X. Yu, and M. Lustig, “High-fidelity direct contrast synthesis from magnetic resonance fingerprinting,” Magnetic Resonance in Medicine, 2023.
  199. “CINENet: deep learning-based 3D cardiac CINE MRI reconstruction with multi-coil complex-valued 4D spatio-temporal convolutions,” Scientific Reports 2020 10:1, vol. 10, pp. 1–13, 8 2020.
  200. C. Qin, J. Schlemper, J. Caballero, A. N. Price, J. V. Hajnal, and D. Rueckert, “Convolutional recurrent neural networks for dynamic MR image reconstruction,” IEEE Transactions on Medical Imaging, vol. 38, pp. 280–290, 1 2019.
  201. P. M. Johnson and M. Drangova, “Conditional generative adversarial network for 3D rigid-body motion correction in MRI,” Magnetic resonance in medicine, vol. 82, no. 3, pp. 901–910, 2019.
  202. Y. Arefeen, J. Xu, M. Zhang, Z. Dong, F. Wang, J. White, B. Bilgic, and E. Adalsteinsson, “Latent signal models: Learning compact representations of signal evolution for improved time-resolved, multi-contrast MRI,” Magnetic Resonance in Medicine, 2023.
  203. S. Biswas, H. K. Aggarwal, and M. Jacob, “Dynamic MRI using model-based deep learning and SToRM priors: MoDL-SToRM,” Magnetic Resonance in Medicine, vol. 82, pp. 485–494, 7 2019.
  204. J. Yoo, K. H. Jin, H. Gupta, J. Yerly, M. Stuber, and M. Unser, “Time-dependent deep image prior for dynamic MRI,” IEEE Transactions on Medical Imaging, vol. 40, no. 12, pp. 3337–3348, 2021.
  205. C. M. Sandino, F. Ong, S. S. Iyer, A. Bush, and S. Vasanawala, “Deep subspace learning for efficient reconstruction of spatiotemporal imaging data,” in NeurIPS 2021 Workshop on Deep Learning and Inverse Problems, 2021.
  206. C. Qin, W. Bai, J. Schlemper, S. E. Petersen, S. K. Piechnik, S. Neubauer, and D. Rueckert, “Joint learning of motion estimation and segmentation for cardiac MR image sequences,” in Medical Image Computing and Computer Assisted Intervention–MICCAI 2018: 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part II 11.    Springer, 2018, pp. 472–480.
  207. S. Ghadimi, D. A. Auger, X. Feng, C. Sun, C. H. Meyer, K. C. Bilchick, J. J. Cao, A. D. Scott, J. N. Oshinski, D. B. Ennis et al., “Fully-automated global and segmental strain analysis of DENSE cardiovascular magnetic resonance using deep learning for segmentation and phase unwrapping,” Journal of Cardiovascular Magnetic Resonance, vol. 23, pp. 1–13, 2021.
  208. C. M. Scannell, M. Veta, A. D. Villa, E. C. Sammut, J. Lee, M. Breeuwer, and A. Chiribiri, “Deep-learning-based preprocessing for quantitative myocardial perfusion MRI,” Journal of Magnetic Resonance Imaging, vol. 51, no. 6, pp. 1689–1696, 2020.
  209. E. J. Zucker, C. M. Sandino, A. Kino, P. Lai, and S. S. Vasanawala, “Free-breathing accelerated cardiac MRI using deep learning: Validation in children and young adults,” Radiology, vol. 300, no. 3, pp. 539–548, 2021.
  210. Q. Zou, A. H. Ahmed, P. Nagal, S. Kruger, and M. Jacob, “Alignment & joint recovery of multi-slice dynamic MRI using deep generative manifold model,” arxiv.org/abs/2101.08196, 2021.
  211. Q. Zou, A. H. Ahmed, P. Nagpal, S. Priya, R. F. Schulte, and M. Jacob, “Variational manifold learning from incomplete data: application to multislice dynamic MRI,” IEEE transactions on medical imaging, vol. 41, no. 12, pp. 3552–3561, 2022.
  212. M. Sermesant, H. Delingette, H. Cochet, P. Jais, and N. Ayache, “Applications of artificial intelligence in cardiovascular imaging,” Nature Reviews Cardiology, vol. 18, no. 8, pp. 600–609, 2021.
  213. Y. Chang, Z. Li, G. Saju, H. Mao, and T. Liu, “Deep learning-based rigid motion correction for magnetic resonance imaging: A survey,” Meta-Radiology, p. 100001, 2023.
  214. X. Zhao and X.-M. Zhao, “Deep learning of brain magnetic resonance images: A brief review,” Methods, vol. 192, pp. 131–140, 2021.
  215. M. W. Haskell, S. F. Cauley, B. Bilgic, J. Hossbach, D. N. Splitthoff, J. Pfeuffer, K. Setsompop, and L. L. Wald, “Network Accelerated Motion Estimation and Reduction (NAMER): Convolutional neural network guided retrospective motion correction using a separable motion model,” Magnetic Resonance in Medicine, vol. 82, pp. 1452–1461, 10 2019.
  216. N. M. Singh, N. Dey, M. Hoffmann, B. Fischl, E. Adalsteinsson, R. Frost, A. V. Dalca, and P. Golland, “Data Consistent Deep Rigid MRI Motion Correction,” Proceedings of Machine Learning Research, vol. 177, pp. 1–14, 1 2023.
  217. H. Eichhorn, K. Hammernik, V. Spieker, S. M. Epp, D. Rueckert, C. Preibisch, and J. A. Schnabel, “Physics-Aware Motion Simulation for T2*-Weighted Brain MRI,” pp. 42–52, 3 2023.
  218. B. Levac, A. Jalal, and J. I. Tamir, “Accelerated motion correction for MRI using score-based generative models,” in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI).    IEEE, 2023, pp. 1–5.
  219. T. Küstner, J. Pan, C. Gilliam, H. Qi, G. Cruz, K. Hammernik, B. Yang, T. Blu, D. Rueckert, R. Botnar et al., “Deep-learning based motion-corrected image reconstruction in 4D magnetic resonance imaging of the body trunk,” in 2020 Asia-Pacific Signal and Information Processing Association Annual Summit and Conference (APSIPA ASC).    IEEE, 2020, pp. 976–985.
  220. X. Wang, M. Uecker, and L. Feng, “Fast real-time cardiac MRI: a review of current techniques and future directions,” Investigative Magnetic Resonance Imaging, vol. 25, no. 4, pp. 252–265, 2021.
  221. A. Singh, S. S. M. Salehi, and A. Gholipour, “Deep predictive motion tracking in magnetic resonance imaging: application to fetal imaging,” IEEE transactions on medical imaging, vol. 39, no. 11, pp. 3523–3534, 2020.
  222. E. Shimron, A. De Goyeneche, K. Wang, A. Halgren, A. B. Syed, S. Vasanawala, and M. Lustig, “BladeNet: Rapid PROPELLER Acquisition and Reconstruction for High Spatio-Temporal Resolution Abdominal MRI,” Proceedings of the 31st Annual International Society for Magnetic Resonance in Medicine, London, UK, pp. 7–12, 2022.
  223. V. Murray, S. Siddiq, C. Crane, M. E. Homsi, T. H. Kim, C. Wu, and R. Otazo, “Movienet: Deep space–time-coil reconstruction network without k-space data consistency for fast motion-resolved 4D MRI,” Magnetic Resonance in Medicine, vol. 91, pp. 600–614, 2 2024.
  224. M. O. Malavé, C. A. Baron, S. P. Koundinyan, C. M. Sandino, F. Ong, J. Y. Cheng, and D. G. Nishimura, “Reconstruction of undersampled 3D non-Cartesian image-based navigators for coronary MRA using an unrolled deep learning model,” Magnetic resonance in medicine, vol. 84, no. 2, pp. 800–812, 2020.
  225. Q. Zou, L. A. Torres, S. B. Fain, N. S. Higano, A. J. Bates, and M. Jacob, “Dynamic imaging using motion-compensated smoothness regularization on manifolds (MoCo-SToRM),” Physics in medicine & biology, vol. 67, no. 14, p. 144001, 2022.
  226. J. N. Freedman, O. J. Gurney-Champion, S. Nill, A.-M. Shiarli, H. E. Bainbridge, H. C. Mandeville, D.-M. Koh, F. McDonald, M. Kachelrieß, U. Oelfke et al., “Rapid 4D-MRI reconstruction using a deep radial convolutional neural network: Dracula,” Radiotherapy and Oncology, vol. 159, pp. 209–217, 2021.
  227. M. L. Terpstra, M. Maspero, F. d’Agata, B. Stemkens, M. P. Intven, J. J. Lagendijk, C. A. Van den Berg, and R. H. Tijssen, “Deep learning-based image reconstruction and motion estimation from undersampled radial k-space for real-time MRI-guided radiotherapy,” Physics in Medicine & Biology, vol. 65, no. 15, p. 155015, 2020.
  228. D. E. Waddington, N. Hindley, N. Koonjoo, C. Chiu, T. Reynolds, P. Z. Liu, B. Zhu, D. Bhutto, C. Paganelli, P. J. Keall et al., “Real-time radial reconstruction with domain transform manifold learning for MRI-guided radiotherapy,” Medical Physics, vol. 50, no. 4, pp. 1962–1974, 2023.
  229. C. M. Sandino, E. K. Cole, C. Alkan, A. S. Chaudhari, A. M. Loening, D. Hyun, J. Dahl, A.-A.-Z. Imran, A. S. Wang, and S. S. Vasanawala, “Upstream Machine Learning in Radiology,” Radiologic Clinics of North America, vol. 59, no. 6, p. 967–985, Nov. 2021.
  230. A. S. Chaudhari, C. M. Sandino, E. K. Cole, D. B. Larson, G. E. Gold, S. S. Vasanawala, M. P. Lungren, B. A. Hargreaves, and C. P. Langlotz, “Prospective Deployment of Deep Learning in MRI: A Framework for Important Considerations, Challenges, and Recommendations for Best Practices,” Journal of Magnetic Resonance Imaging, vol. 54, no. 2, p. 357–371, Aug. 2020.
  231. R. Zhao, B. Yaman, Y. Zhang, R. Stewart, A. Dixon, F. Knoll, Z. Huang, Y. W. Lui, M. S. Hansen, and M. P. Lungren, “fastMRI+, Clinical pathology annotations for knee and brain fully sampled magnetic resonance imaging data,” Scientific Data, vol. 9, no. 1, Apr. 2022.
  232. R. Zhao, Y. Zhang, B. Yaman, M. P. Lungren, and M. S. Hansen, “End-to-End AI-based MRI Reconstruction and Lesion Detection Pipeline for Evaluation of Deep Learning Image Reconstruction,” 2021.
  233. T. Weber, M. Ingrisch, B. Bischl, and D. Rügamer, “Constrained Probabilistic Mask Learning for Task-Specific Undersampled MRI Reconstruction,” in Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), January 2024, pp. 7665–7674.
  234. A. D. Desai, F. Caliva, C. Iriondo, A. Mortazi, S. Jambawalikar, U. Bagci, M. Perslev, C. Igel, E. B. Dam, S. Gaj, M. Yang, X. Li, C. M. Deniz, V. Juras, R. Regatte, G. E. Gold, B. A. Hargreaves, V. Pedoia, A. S. Chaudhari, N. Khosravan, D. Torigian, J. Ellermann, M. Akcakaya, R. Tibrewala, I. Flament, M. O’Brien, S. Majumdar, K. Nakamura, and A. Pai, “The International Workshop on Osteoarthritis Imaging Knee MRI Segmentation Challenge: A Multi-Institute Evaluation and Analysis Framework on a Standardized Dataset,” Radiology: Artificial Intelligence, vol. 3, no. 3, p. e200078, May 2021.
  235. A. M. Schmidt, A. D. Desai, L. E. Watkins, H. A. Crowder, M. S. Black, V. Mazzoli, E. B. Rubin, Q. Lu, J. W. MacKay, R. D. Boutin, F. Kogan, G. E. Gold, B. A. Hargreaves, and A. S. Chaudhari, “Generalizability of Deep Learning Segmentation Algorithms for Automated Assessment of Cartilage Morphology and ¡scp¿MRI¡/scp¿ Relaxometry,” Journal of Magnetic Resonance Imaging, vol. 57, no. 4, p. 1029–1039, Jul. 2022.
  236. Z. Wu, T. Yin, Y. Sun, R. Frost, A. van der Kouwe, A. V. Dalca, and K. L. Bouman, “Learning Task-Specific Strategies for Accelerated MRI,” 2023.
  237. M. Uecker et al., “ESPIRiT—an eigenvalue approach to autocalibrating parallel MRI: where SENSE meets GRAPPA,” Magnetic Resonance in Medicine, vol. 71, no. 3, pp. 990–1001, 2014.
  238. M. Uecker, T. Hohage, K. T. Block, and J. Frahm, “Image reconstruction by regularized nonlinear inversion—joint estimation of coil sensitivities and image content,” Magnetic Resonance in Medicine, vol. 60, no. 3, pp. 674–682, 2008.
  239. L. Ying and J. Sheng, “Joint image reconstruction and sensitivity estimation in SENSE (JSENSE),” Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine, vol. 57, no. 6, pp. 1196–1202, 2007.
  240. A. Sriram, J. Zbontar, T. Murrell, A. Defazio, C. L. Zitnick, N. Yakubova, F. Knoll, and P. Johnson, “End-to-end variational networks for accelerated MRI reconstruction,” in Medical Image Computing and Computer Assisted Intervention–MICCAI 2020: 23rd International Conference, Lima, Peru, October 4–8, 2020, Proceedings, Part II 23.    Springer, 2020, pp. 64–73.
  241. Y. Jun, H. Shin, T. Eo, and D. Hwang, “Joint deep model-based MR image and coil sensitivity reconstruction network (joint-ICNet) for fast MRI,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2021, pp. 5270–5279.
  242. G. Luo, X. Wang, V. Roeloffs, Z. Tan, and M. Uecker, “Joint estimation of coil sensitivities and image content using a deep image prior,” in Proceedings of the 29th Annual Meeting of ISMRM, 2021, p. 280.
  243. M. Zhang, J. Xu, Y. Arefeen, and E. Adalsteinsson, “Zero-Shot Self-Supervised Joint Temporal Image and Sensitivity Map Reconstruction via Linear Latent Space,” arXiv preprint arXiv:2303.02254, 2023.
  244. J. Liu, S. Pasumarthi, B. Duffy, E. Gong, K. Datta, and G. Zaharchuk, “One model to synthesize them all: Multi-contrast multi-scale transformer for missing data imputation,” IEEE Transactions on Medical Imaging, 2023.
  245. B. Sveinsson, A. S. Chaudhari, B. Zhu, N. Koonjoo, M. Torriani, G. E. Gold, and M. S. Rosen, “Synthesizing quantitative T2 maps in right lateral knee femoral condyles from multicontrast anatomic data with a conditional generative adversarial network,” Radiology: Artificial Intelligence, vol. 3, no. 5, p. e200122, 2021.
  246. C. Zhao, M. Shao, A. Carass, H. Li, B. E. Dewey, L. M. Ellingsen, J. Woo, M. A. Guttman, A. M. Blitz, M. Stone et al., “Applications of a deep learning method for anti-aliasing and super-resolution in MRI,” Magnetic resonance imaging, vol. 64, pp. 132–141, 2019.
  247. Y. Li, B. Sixou, and F. Peyrin, “A review of the deep learning methods for medical images super resolution problems,” Irbm, vol. 42, no. 2, pp. 120–133, 2021.
  248. M. W. Haskell, J.-F. Nielsen, and D. C. Noll, “Off-resonance artifact correction for mri: A review,” NMR in Biomedicine, vol. 36, no. 5, p. e4867, 2023.
  249. R. Ayde, T. Senft, N. Salameh, and M. Sarracanie, “Deep learning for fast low-field MRI acquisitions,” Scientific reports, vol. 12, no. 1, p. 11394, 2022.
  250. N. Koonjoo, B. Zhu, G. C. Bagnall, D. Bhutto, and M. Rosen, “Boosting the signal-to-noise of low-field MRI with deep learning image reconstruction,” Scientific reports, vol. 11, no. 1, pp. 1–16, 2021.
  251. K. Lei, A. B. Syed, X. Zhu, J. M. Pauly, and S. V. Vasanawala, “Automated MRI field of view prescription from region of interest prediction by intra-stack attention neural network,” Bioengineering, vol. 10, no. 1, p. 92, 2023.
  252. L. C. Bell, E. Shimron, and D. W. S. S. Francisco, “Sharing Data Is Essential for the Future of AI in Medical Imaging,” Radiology: Artificial Intelligence, 11 2023.
  253. Z. Ramzi, P. Ciuciu, and J.-L. Starck, “Benchmarking Deep Nets MRI Reconstruction Models on the FastMRI Publicly Available Dataset,” in ISBI 2020 - International Symposium on Biomedical Imaging, 2020.
  254. Y. Lim, A. Toutios, Y. Bliesener, Y. Tian, S. G. Lingala, C. Vaz, T. Sorensen, M. Oh, S. Harper, W. Chen et al., “A multispeaker dataset of raw and reconstructed speech production real-time MRI video and 3D volumetric images,” Scientific data, vol. 8, no. 1, pp. 1–14, 2021.
  255. C. C. et al., “OCMR (v1.0)–Open-Access Multi-Coil k-Space Dataset for Cardiovascular Magnetic Resonance Imaging,” arXiv: 2008.03410v2, 2020.
  256. M. Lyu, L. Mei, S. Huang, S. Liu, Y. Li, K. Yang, Y. Liu, Y. Dong, L. Dong, and E. X. Wu, “M4Raw: A multi-contrast, multi-repetition, multi-channel MRI k-space dataset for low-field MRI research,” Scientific Data, vol. 10, no. 1, p. 264, 2023.
  257. “The Human Connectome Project, University of Souterhn California,,” http://www.humanconnectomeproject.org/, 2011, accessed: 2021-03-22. [Online]. Available: http://www.humanconnectomeproject.org/
  258. “IXI dataset,” http://brain-development.org/ixi-dataset/, 2010, accessed: 2021-03-22. [Online]. Available: http://brain-development.org/ixi-dataset/
  259. B. H. Menze, A. Jakab, S. Bauer, J. Kalpathy-Cramer, K. Farahani, J. Kirby, Y. Burren, N. Porz, J. Slotboom, R. Wiest et al., “The multimodal brain tumor image segmentation benchmark (BRATS),” IEEE transactions on medical imaging, vol. 34, no. 10, pp. 1993–2024, 2014.
  260. M. Ghaffari, A. Sowmya, and R. Oliver, “Automated brain tumor segmentation using multimodal brain scans: a survey based on models submitted to the BraTS 2012–2018 challenges,” IEEE reviews in biomedical engineering, vol. 13, pp. 156–168, 2019.
  261. C. R. Jack Jr, M. A. Bernstein, N. C. Fox, P. Thompson, G. Alexander, D. Harvey, B. Borowski, P. J. Britson, J. L. Whitwell, C. Ward et al., “The Alzheimer’s disease neuroimaging initiative (ADNI): MRI methods,” Journal of Magnetic Resonance Imaging: An Official Journal of the International Society for Magnetic Resonance in Medicine, vol. 27, no. 4, pp. 685–691, 2008.
  262. W. Ollier, T. Sprosen, and T. Peakman, “UK Biobank: from concept to reality,” 2005.
  263. B. Kurdi, S. Lozano, and M. R. Banaji, “Introducing the open affective standardized image set (OASIS),” Behavior research methods, vol. 49, pp. 457–470, 2017.
  264. A. Paszke et al., “PyTorch: An imperative style, high-performance deep learning library,” Advances in Neural Information Processing Systems, vol. 32, 2019.
  265. M. Abadi, A. Agarwal, P. Barham, E. Brevdo, Z. Chen, C. Citro, G. S. Corrado, A. Davis, J. Dean, M. Devin et al., “TensorFlow: Large-scale machine learning on heterogeneous systems,” 2015, software available from tensorflow.org. [Online]. Available: https://www.tensorflow.org/
  266. M. Uecker et al., “Berkeley advanced reconstruction toolbox,” in Proc. Intl. Soc. Mag. Reson. Med, vol. 23, no. 2486, 2015.
  267. M. Blumenthal, G. Luo, M. Schilling, H. C. M. Holme, and M. Uecker, “Deep, deep learning with BART,” Magnetic Resonance in Medicine, vol. 89, no. 2, pp. 678–693, 2023.
  268. M. S. Hansen and T. S. Sørensen, “Gadgetron: an open source framework for medical image reconstruction,” Magnetic resonance in medicine, vol. 69, no. 6, pp. 1768–1776, 2013.
  269. F. Ong and M. Lustig, “SigPy: a python package for high performance iterative reconstruction,” in Proc. Intl. Soc. Mag. Reson. Med, vol. 4819, 2019.
  270. K. J. Layton, S. Kroboth, F. Jia, S. Littin, H. Yu, J. Leupold, J.-F. Nielsen, T. Stöcker, and M. Zaitsev, “Pulseq: a rapid and hardware-independent pulse sequence prototyping framework,” Magnetic resonance in medicine, vol. 77, no. 4, pp. 1544–1552, 2017.
  271. K. Herz, S. Mueller, O. Perlman, M. Zaitsev, L. Knutsson, P. Z. Sun, J. Zhou, P. van Zijl, K. Heinecke, P. Schuenke et al., “Pulseq-CEST: Towards multi-site multi-vendor compatibility and reproducibility of CEST experiments using an open-source sequence standard,” Magnetic resonance in medicine, vol. 86, no. 4, pp. 1845–1858, 2021.
  272. L. Ning, E. Bonet-Carne, F. Grussu, F. Sepehrband, E. Kaden, J. Veraart, S. B. Blumberg, C. S. Khoo, M. Palombo, I. Kokkinos et al., “Cross-scanner and cross-protocol multi-shell diffusion MRI data harmonization: Algorithms and results,” Neuroimage, vol. 221, p. 117128, 2020.
  273. A. Karakuzu, M. Boudreau, T. Duval, T. Boshkovski, I. Leppert, J.-F. Cabana, I. Gagnon, P. Beliveau, G. Pike, J. Cohen-Adad et al., “qMRLab: Quantitative MRI analysis, under one umbrella,” Journal of Open Source Software, vol. 5, no. 53, 2020.
  274. S. J. Inati, J. D. Naegele, N. R. Zwart, V. Roopchansingh, M. J. Lizak, D. C. Hansen, C.-Y. Liu, D. Atkinson, P. Kellman, S. Kozerke et al., “ISMRM Raw data format: A proposed standard for MRI raw datasets,” Magnetic resonance in medicine, vol. 77, no. 1, pp. 411–421, 2017.
  275. G. Elmas, S. U. Dar, Y. Korkmaz, E. Ceyani, B. Susam, M. Ozbey, S. Avestimehr, and T. Çukur, “Federated learning of generative image priors for MRI reconstruction,” IEEE Transactions on Medical Imaging, 2022.
  276. B. R. Levac, M. Arvinte, and J. I. Tamir, “Federated End-to-End Unrolled Models for Magnetic Resonance Image Reconstruction,” Bioengineering, vol. 10, no. 3, p. 364, 2023.
  277. P. M. Johnson, G. Jeong, K. Hammernik, J. Schlemper, C. Qin, J. Duan, D. Rueckert, J. Lee, N. Pezzotti, E. De Weerdt et al., “Evaluation of the robustness of learned MR image reconstruction to systematic deviations between training and test data for the models from the fastMRI challenge,” in Machine Learning for Medical Image Reconstruction: 4th International Workshop, MLMIR 2021, Held in Conjunction with MICCAI 2021, Strasbourg, France, October 1, 2021, Proceedings 4.    Springer, 2021, pp. 25–34.
  278. M. Z. Darestani, A. Chaudhari, and R. Heckel, “Measuring Robustness in Deep Learning Based Compressive Sensing,” arXiv preprint arXiv:2102.06103, 2021.
  279. N. Avidan and M. Freiman, “Physically-primed deep-neural-networks for generalized undersampled MRI reconstruction,” arXiv preprint arXiv:2209.00462, 2022.
  280. F. Knoll, K. Hammernik, E. Kobler, T. Pock, M. P. Recht, and D. K. Sodickson, “Assessment of the generalization of learned image reconstruction and the potential for transfer learning,” Magnetic resonance in medicine, vol. 81, no. 1, pp. 116–128, 2019.
  281. J. Huang, S. Wang, G. Zhou, W. Hu, and G. Yu, “Evaluation on the generalization of a learned convolutional neural network for MRI reconstruction,” Magnetic Resonance Imaging, vol. 87, pp. 38–46, 2022.
  282. S. U. H. Dar, M. Özbey, A. B. Çatlı, and T. Çukur, “A transfer-learning approach for accelerated MRI using deep neural networks,” Magnetic resonance in medicine, vol. 84, no. 2, pp. 663–685, 2020.
  283. K. Lin and R. Heckel, “Robustness of Deep Learning for Accelerated MRI: Benefits of Diverse Training Data,” arXiv preprint arXiv:2312.10271, 2023.
  284. G. Varoquaux and V. Cheplygina, “Machine learning for medical imaging: methodological failures and recommendations for the future,” NPJ digital medicine, vol. 5, no. 1, p. 48, 2022.
  285. L. Seyyed-Kalantari, H. Zhang, M. B. McDermott, I. Y. Chen, and M. Ghassemi, “Underdiagnosis bias of artificial intelligence algorithms applied to chest radiographs in under-served patient populations,” Nature medicine, vol. 27, no. 12, pp. 2176–2182, 2021.
  286. R. J. Chen, J. J. Wang, D. F. Williamson, T. Y. Chen, J. Lipkova, M. Y. Lu, S. Sahai, and F. Mahmood, “Algorithmic fairness in artificial intelligence for medicine and healthcare,” Nature Biomedical Engineering, vol. 7, no. 6, pp. 719–742, 2023.
  287. E. Shimron, J. I. Tamir, K. Wang, and M. Lustig, “Implicit data crimes: Machine learning bias arising from misuse of public data,” Proceedings of the National Academy of Sciences, vol. 119, no. 13, p. e2117203119, 2022.
  288. N. Deveshwar, A. Rajagopal, S. Sahin, E. Shimron, and P. E. Larson, “Synthesizing Complex-Valued Multicoil MRI Data from Magnitude-Only Images,” Bioengineering, vol. 10, no. 3, p. 358, 2023.
  289. Q. Yang, Y. Lin, J. Wang, J. Bao, X. Wang, L. Ma, Z. Zhou, Q. Yang, S. Cai, H. He et al., “Model-based synthetic data-driven learning (MOST-DL): Application in single-shot T 2 mapping with severe head motion using overlapping-echo acquisition,” IEEE Transactions on Medical Imaging, vol. 41, no. 11, pp. 3167–3181, 2022.
  290. G. Luo, X. Wang, M. Blumenthal, M. Schilling, E. H. U. Rauf, R. Kotikalapudi, N. Focke, and M. Uecker, “Generative Image Priors for MRI Reconstruction Trained from Magnitude-Only Images,” arXiv preprint arXiv:2308.02340, 2023.
  291. C. Zhang, Q. Yang, L. Fan, S. Yu, L. Sun, C. Cai, and X. Ding, “Towards better generalization using synthetic data: A domain adaptation framework for t 2 mapping via multiple overlapping-echo acquisition,” IEEE Transactions on Medical Imaging, 2023.
  292. S. Bhadra, V. A. Kelkar, F. J. Brooks, and M. A. Anastasio, “On hallucinations in tomographic image reconstruction,” IEEE transactions on medical imaging, vol. 40, no. 11, pp. 3249–3260, 2021.
  293. J. P. Cohen, M. Luck, and S. Honari, “Distribution matching losses can hallucinate features in medical image translation,” in Medical Image Computing and Computer Assisted Intervention–MICCAI 2018: 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part I.    Springer, 2018, pp. 529–536.
  294. N. M. Gottschling, V. Antun, B. Adcock, and A. C. Hansen, “The troublesome kernel: why deep learning for inverse problems is typically unstable,” arXiv preprint arXiv:2001.01258, 2020.
  295. Y. Huang, T. Würfl, K. Breininger, L. Liu, G. Lauritsch, and A. Maier, “Some investigations on robustness of deep learning in limited angle tomography,” in International Conference on Medical Image Computing and Computer-Assisted Intervention.    Springer, 2018, pp. 145–153.
  296. V. Antun, F. Renna, C. Poon, B. Adcock, and A. C. Hansen, “On instabilities of deep learning in image reconstruction and the potential costs of ai,” Proceedings of the National Academy of Sciences, vol. 117, no. 48, pp. 30 088–30 095, 2020.
  297. A. Krainovic, M. Soltanolkotabi, and R. Heckel, “Learning Provably Robust Estimators for Inverse Problems via Jittering,” 2023.
  298. J. N. Morshuis, S. Gatidis, M. Hein, and C. F. Baumgartner, “Adversarial robustness of MR image reconstruction under realistic perturbations,” in International Workshop on Machine Learning for Medical Image Reconstruction.    Springer, 2022, pp. 24–33.
  299. A. Goujon, S. Neumayer, P. Bohra, S. Ducotterd, and M. Unser, “A neural-network-based convex regularizer for inverse problems,” IEEE Transactions on Computational Imaging, 2023.
  300. M. John, J. R. Chand, and M. Jacob, “Local monotone operator learning using non-monotone operators: MnM-MOL,” arXiv preprint arXiv:2312.00386, 2023.
  301. F. Calivá, K. Cheng, R. Shah, and V. Pedoia, “Adversarial robust training of deep learning MRI reconstruction models,” arXiv preprint arXiv:2011.00070, 2020.
  302. K. Cheng, F. Calivá, R. Shah, M. Han, S. Majumdar, and V. Pedoia, “Addressing the False Negative Problem of Deep Learning MRI Reconstruction Models by Adversarial Attacks and Robust Training,” 2020, pp. 121–135.
  303. Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Transactions on Image Processing, vol. 13, no. 4, pp. 600–612, 2004.
  304. A. Mason, J. Rioux, S. E. Clarke, A. Costa, M. Schmidt, V. Keough, T. Huynh, and S. Beyea, “Comparison of objective image quality metrics to expert radiologists’ scoring of diagnostic quality of MR images,” IEEE transactions on medical imaging, vol. 39, no. 4, pp. 1064–1072, 2019.
  305. J. Johnson, A. Alahi, and L. Fei-Fei, “Perceptual losses for real-time style transfer and super-resolution,” in Computer Vision–ECCV 2016: 14th European Conference, Amsterdam, The Netherlands, October 11-14, 2016, Proceedings, Part II 14.    Springer, 2016, pp. 694–711.
  306. P. M. Adamson, A. D. Desai, J. Dominic, C. Bluethgen, J. P. Wood, A. B. Syed, R. D. Boutin, K. J. Stevens, S. Vasanawala, J. M. Pauly et al., “Using Deep Feature Distances for Evaluating MR Image Reconstruction Quality,” in NeurIPS 2023 Workshop on Deep Learning and Inverse Problems, 2023.
  307. K. Wang, J. I. Tamir, A. D. Goyeneche, U. Wollner, R. Brada, S. X. Yu, and M. Lustig, “High fidelity deep learning-based MRI reconstruction with instance-wise discriminative feature matching loss,” Magnetic Resonance in Medicine, vol. 88, pp. 476–491, 7 2022.
  308. R. Zhang, P. Isola, A. A. Efros, E. Shechtman, and O. Wang, “The Unreasonable Effectiveness of Deep Features as a Perceptual Metric,” 2018.
  309. P. M. Adamson, B. Gunel, J. Dominic, A. D. Desai, D. Spielman, S. Vasanawala, J. M. Pauly, and A. Chaudhari, “SSFD: Self-supervised feature distance as an MR image reconstruction quality metric,” in NeurIPS 2021 Workshop on Deep Learning and Inverse Problems, 2021.
  310. A. S. Chaudhari, F. Kogan, V. Pedoia, S. Majumdar, G. E. Gold, and B. A. Hargreaves, “Rapid Knee MRI Acquisition and Analysis Techniques for Imaging Osteoarthritis,” Journal of Magnetic Resonance Imaging, vol. 52, no. 5, p. 1321–1339, Nov. 2019.
  311. A. S. Chaudhari, M. J. Grissom, Z. Fang, B. Sveinsson, J. H. Lee, G. E. Gold, B. A. Hargreaves, and K. J. Stevens, “Diagnostic accuracy of quantitative multicontrast 5-minute knee MRI using prospective artificial intelligence image quality enhancement,” AJR. American journal of roentgenology, vol. 216, no. 6, p. 1614, 2021.
  312. K. C. Tezcan, N. Karani, C. F. Baumgartner, and E. Konukoglu, “Sampling possible reconstructions of undersampled acquisitions in MR imaging with a deep learned prior,” IEEE Transactions on Medical Imaging, vol. 41, no. 7, pp. 1885–1896, 2022.
  313. V. Edupuganti, M. Mardani, S. Vasanawala, and J. Pauly, “Uncertainty quantification in deep MRI reconstruction,” IEEE Transactions on Medical Imaging, vol. 40, no. 1, pp. 239–250, 2020.
  314. D. Narnhofer, A. Effland, E. Kobler, K. Hammernik, F. Knoll, and T. Pock, “Bayesian uncertainty estimation of learned variational MRI reconstruction,” IEEE Transactions on Medical Imaging, vol. 41, no. 2, pp. 279–291, 2021.
  315. T. Küstner, K. Hammernik, D. Rueckert, T. Hepp, and S. Gatidis, “Predictive uncertainty in deep learning-based MR image reconstruction using deep ensembles: Evaluation on the fastMRI data set.” Magnetic Resonance in Medicine, 2024.
  316. K. Wang, A. Angelopoulos, A. De Goyeneche, A. Kohli, E. Shimron, S. Yu, J. Malik, and M. Lustig, “Rigorous Uncertainty Estimation for MRI Reconstruction.”
  317. Y. Gal and Z. Ghahramani, “Dropout as a bayesian approximation: Representing model uncertainty in deep learning,” in international conference on machine learning.    PMLR, 2016, pp. 1050–1059.
  318. Z. Zhang, A. Romero, M. J. Muckley, P. Vincent, L. Yang, and M. Drozdzal, “Reducing uncertainty in undersampled MRI reconstruction with active acquisition,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2019, pp. 2049–2058.
  319. P. Fischer, K. Thomas, and C. F. Baumgartner, “Uncertainty Estimation and Propagation in Accelerated MRI Reconstruction,” in International Workshop on Uncertainty for Safe Utilization of Machine Learning in Medical Imaging.    Springer, 2023, pp. 84–94.
  320. T. Chen, B. Xu, C. Zhang, and C. Guestrin, “Training deep nets with sublinear memory cost,” arXiv preprint arXiv:1604.06174, 2016.
  321. M. Kellman, K. Zhang, E. Markley, J. Tamir, E. Bostan, M. Lustig, and L. Waller, “Memory-efficient learning for large-scale computational imaging,” IEEE Transactions on Computational Imaging, vol. 6, pp. 1403–1414, 2020.
  322. S. Bai, J. Z. Kolter, and V. Koltun, “Deep equilibrium models,” Advances in Neural Information Processing Systems, vol. 32, 2019.
User Edit Pencil Streamline Icon: https://streamlinehq.com
Authors (5)
  1. Reinhard Heckel (74 papers)
  2. Mathews Jacob (72 papers)
  3. Akshay Chaudhari (34 papers)
  4. Or Perlman (10 papers)
  5. Efrat Shimron (8 papers)
Citations (3)