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Quantitative molecular imaging using deep magnetic resonance fingerprinting

Nature Protocols volume 20, pages 3024–3054 (2025)Cite this article

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Abstract

Deep learning-based saturation transfer magnetic resonance fingerprinting (MRF) is an emerging approach for noninvasive in vivo imaging of proteins, metabolites and pH. It involves a series of steps, including sample/participant preparation, image acquisition schedule design, biophysical model formulation and artificial intelligence and computational model training, followed by image acquisition, deep reconstruction and analysis. Saturation transfer-based molecular MRI has been slow to reach clinical maturity and adoption for clinical practice due to its technical complexity, semi-quantitative contrast-weighted nature and long scan times needed for the extraction of quantitative molecular biomarkers. Deep MRF provides solutions to these challenges by providing a quantitative and rapid framework for extracting biologically and clinically meaningful molecular information. Here we define a complete protocol for quantitative molecular MRI using deep MRF. We describe in vitro sample preparation and animal and human scan considerations, and provide intuition behind the acquisition protocol design and optimization of chemical exchange saturation transfer (CEST) and semi-solid magnetization transfer (MT) quantitative imaging. We then extensively describe the building blocks for several artificial intelligence models and demonstrate their performance for different applications, including cancer monitoring, brain myelin imaging and pH quantification. Finally, we provide guidelines to further modify and expand the pipeline for imaging a variety of other pathologies (such as neurodegeneration, stroke and cardiac disease), accompanied by the related open-source code and sample data. The procedure takes between 48 min (for two proton pools or in vitro imaging) and 57 h (for complex multi-proton pool in vivo imaging) to complete and is suitable for graduate student-level users.

Key points

  • The procedure includes in vitro sample preparation, animal and human scan considerations, acquisition protocol design, and optimization of chemical exchange saturation transfer and semi-solid magnetization transfer quantitative imaging. We include artificial intelligence models for diagnostic applications.

  • Deep magnetic resonance fingerprinting does not require steady-state imaging conditions, enabling a reduction in scan time when compared with QUESP/QUEST, QUESTRA, Omega Plot, BM fitting, multi-pool Lorentzian fitting or chemical exchange saturation transfer-weighted imaging.

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Fig. 1: Practical overview of the deep molecular MRF protocol.
Fig. 2: Experimental validation pipeline for CEST–MRF.
Fig. 3: A typical CEST–MRF pulse sequence diagram.
Fig. 4: Sequential learning of multi-proton pool information.
Fig. 5: Unsupervised learning-based MRF reconstruction.
Fig. 6: Dot product-based parameter quantification example.
Fig. 7: Quantitative parameter maps reconstructed using sequential neural networks30.
Fig. 8: Quantitative parameter maps from a healthy human volunteer scanned at 3T, obtained using a supervised and deep reconstruction network42.
Fig. 9: Quantitative semi-solid MT and water proton pool parameter maps from a healthy human volunteer scanned at 3T, obtained using an unsupervised deep learning approach41.

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Data availability

All the data used in this work are available at https://github.com/momentum-laboratory/deep-molecular-mrf and https://doi.org/10.5281/zenodo.14211516. They include raw MRF data, quantitative parameter maps (Figs. 6–9), a CAD file for 3D printing a six-vial (phantom) holder and pulse sequence files (Table 2). A complete preclinical CEST–MRF pulse sequence for Bruker scanners is available at https://osf.io/52bsg (Paravision 6) and https://github.com/dkorenchan/cest-mrf-image-recon/tree/main/Bruker_PulseSequenceFiles/PV360_3_5 (Paravision 360). The .seq format files used in this work were also deposited at the pulseq CEST open library at https://github.com/kherz/pulseq-cest-library/tree/master/seq-library.

Code availability

All code is available on https://github.com/momentum-laboratory/deep-molecular-mrf and https://doi.org/10.5281/zenodo.14211516 in the format of Python scripts and Jupyter notebooks.

References

  1. Ward, K., Aletras, A. & Balaban, R. S. A new class of contrast agents for MRI based on proton chemical exchange dependent saturation transfer (CEST). J. Magn. Reson. 143, 79–87 (2000).

    Article  CAS  PubMed  Google Scholar 

  2. Zaiss, M. & Bachert, P. Chemical exchange saturation transfer (CEST) and MR Z-spectroscopy in vivo: a review of theoretical approaches and methods. Phys. Med. Biol. 58, R221 (2013).

    Article  PubMed  Google Scholar 

  3. Van Zijl, P. C. & Yadav, N. N. Chemical exchange saturation transfer (CEST): what is in a name and what isn’t? Magn. Reson. Med. 65, 927–948 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Zhou, J., Payen, J.-F., Wilson, D. A., Traystman, R. J. & Van Zijl, P. C. Using the amide proton signals of intracellular proteins and peptides to detect pH effects in MRI. Nat. Med. 9, 1085–1090 (2003).

    Article  CAS  PubMed  Google Scholar 

  5. Wang, E. et al. Mapping tissue pH in an experimental model of acute stroke—determination of graded regional tissue pH changes with non-invasive quantitative amide proton transfer MRI. Neuroimage 191, 610–617 (2019).

    Article  PubMed  Google Scholar 

  6. Wang, E. et al. pH imaging reveals worsened tissue acidification in diffusion kurtosis lesion than the kurtosis/diffusion lesion mismatch in an animal model of acute stroke. J. Cereb. Blood Flow Metab. 37, 3325–3333 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Heo, H.-Y. et al. Improving the detection sensitivity of pH-weighted amide proton transfer MRI in acute stroke patients using extrapolated semisolid magnetization transfer reference signals. Magn. Reson. Med. 78, 871–880 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Heo, H.-Y., Tee, Y. K., Harston, G., Leigh, R. & Chappell, M. A. Amide proton transfer imaging in stroke. NMR Biomed. 36, e4734 (2023).

    Article  CAS  PubMed  Google Scholar 

  9. Ma, B. et al. Applying amide proton transfer-weighted MRI to distinguish pseudoprogression from true progression in malignant gliomas. J. Magn. Reson. Imaging 44, 456–462 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Mehrabian, H., Desmond, K. L., Soliman, H., Sahgal, A. & Stanisz, G. J. Differentiation between radiation necrosis and tumor progression using chemical exchange saturation transfer. Clin. Cancer Res. 23, 3667–3675 (2017).

    Article  CAS  PubMed  Google Scholar 

  11. Zhou, J., Heo, H.-Y., Knutsson, L., van Zijl, P. C. & Jiang, S. APT-weighted MRI: techniques, current neuro applications, and challenging issues. J. Magn. Reson. Imaging 50, 347–364 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Cai, K. et al. Magnetic resonance imaging of glutamate. Nat. Med. 18, 302–306 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Crescenzi, R. et al. In vivo measurement of glutamate loss is associated with synapse loss in a mouse model of tauopathy. Neuroimage 101, 185–192 (2014).

    Article  CAS  PubMed  Google Scholar 

  14. Haris, M. et al. Imaging of glutamate neurotransmitter alterations in Alzheimer’s disease. NMR Biomed. 26, 386–391 (2013).

    Article  CAS  PubMed  Google Scholar 

  15. Wang, K. et al. Lateralization of temporal lobe epileptic foci with automated chemical exchange saturation transfer measurements at 3 Tesla. eBioMedicine 89, 104460 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Neal, A. et al. Glutamate-weighted imaging contrast in gliomas with 7 Tesla magnetic resonance imaging. Neuroimage Clin. 22, 101694 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Haris, M. et al. A technique for in vivo mapping of myocardial creatine kinase metabolism. Nat. Med. 20, 209–214 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. AlGhuraibawi, W. et al. CEST MRI reveals a correlation between visceral fat mass and reduced myocardial creatine in obese individuals despite preserved ventricular structure and function. NMR Biomed. 32, e4104 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Gilad, A. A. et al. Artificial reporter gene providing MRI contrast based on proton exchange. Nat. Biotechnol. 25, 217–219 (2007).

    Article  CAS  PubMed  Google Scholar 

  20. Gilad, A. A., Bar-Shir, A., Bricco, A. R., Mohanta, Z. & McMahon, M. T. Protein and peptide engineering for chemical exchange saturation transfer imaging in the age of synthetic biology. NMR Biomed. 36, e4712 (2023).

    Article  PubMed  Google Scholar 

  21. Perlman, O. et al. Redesigned reporter gene for improved proton exchange-based molecular MRI contrast. Sci. Rep. 10, 20664 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Farrar, C. T. et al. Establishing the lysine-rich protein CEST reporter gene as a CEST MR imaging detector for oncolytic virotherapy. Radiology 275, 746–754 (2015).

    Article  PubMed  Google Scholar 

  23. Meier, S. et al. Non-invasive detection of adeno-associated viral gene transfer using a genetically encoded CEST–MRI reporter gene in the murine heart. Sci. Rep. 8, 4638 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  24. Wike-Hooley, J., Haveman, J. & Reinhold, H. The relevance of tumour pH to the treatment of malignant disease. Radiother. Oncol. 2, 343–366 (1984).

    Article  CAS  PubMed  Google Scholar 

  25. Webb, B. A., Chimenti, M., Jacobson, M. P. & Barber, D. L. Dysregulated pH: a perfect storm for cancer progression. Nat. Rev. Cancer 11, 671–677 (2011).

    Article  CAS  PubMed  Google Scholar 

  26. Corbet, C. & Feron, O. Tumour acidosis: from the passenger to the driver’s seat. Nat. Rev. Cancer 17, 577–593 (2017).

    Article  CAS  PubMed  Google Scholar 

  27. Lim, H., Albatany, M., Martı́nez-Santiesteban, F., Bartha, R. & Scholl, T. J. Longitudinal measurements of intra-and extracellular pH gradient in a rat model of glioma. Tomography 4, 46–54 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  28. Walsh, J. J. et al. Imaging hallmarks of the tumor microenvironment in glioblastoma progression. Front. Oncol. 11, 692650 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Nilsson, C., Johansson, U., Johansson, A.-C., Kaagedal, K. & Öllinger, K. Cytosolic acidification and lysosomal alkalinization during TNF-α induced apoptosis in U937 cells. Apoptosis 11, 1149–1159 (2006).

    Article  CAS  PubMed  Google Scholar 

  30. Perlman, O. et al. Quantitative imaging of apoptosis following oncolytic virotherapy by magnetic resonance fingerprinting aided by deep learning. Nat. Biomed. Eng. 6, 648–657 (2022).

    Article  CAS  PubMed  Google Scholar 

  31. Ma, D. et al. Magnetic resonance fingerprinting. Nature 495, 187–192 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Cohen, O., Huang, S., McMahon, M. T., Rosen, M. S. & Farrar, C. T. Rapid and quantitative chemical exchange saturation transfer (CEST) imaging with magnetic resonance fingerprinting (MRF). Magn. Reson. Med. 80, 2449–2463 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Zhou, Z. et al. Chemical exchange saturation transfer fingerprinting for exchange rate quantification. Magn. Reson. Med. 80, 1352–1363 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  34. Heo, H.-Y. et al. Quantifying amide proton exchange rate and concentration in chemical exchange saturation transfer imaging of the human brain. Neuroimage 189, 202–213 (2019).

    Article  CAS  PubMed  Google Scholar 

  35. Bipin Mehta, B. et al. Magnetic resonance fingerprinting: a technical review. Magn. Reson. Med. 81, 25–46 (2019).

    Article  PubMed  Google Scholar 

  36. McGivney, D. F. et al. SVD compression for magnetic resonance fingerprinting in the time domain. IEEE Trans. Med. Imaging 33, 2311–2322 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  37. Cauley, S. F. et al. Fast group matching for MR fingerprinting reconstruction. Magn. Reson. Med. 74, 523–528 (2015).

    Article  PubMed  Google Scholar 

  38. Yang, M. et al. Low rank approximation methods for MR fingerprinting with large scale dictionaries. Magn. Reson. Med. 79, 2392–2400 (2018).

    Article  PubMed  Google Scholar 

  39. Cohen, O., Zhu, B. & Rosen, M. S. MR fingerprinting deep reconstruction network (DRONE). Magn. Reson. Med. 80, 885–894 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Kim, B., Schär, M., Park, H. & Heo, H.-Y. A deep learning approach for magnetization transfer contrast MR fingerprinting and chemical exchange saturation transfer imaging. Neuroimage 221, 117165 (2020).

    Article  CAS  PubMed  Google Scholar 

  41. Kang, B., Kim, B., Schär, M., Park, H. & Heo, H.-Y. Unsupervised learning for magnetization transfer contrast MR fingerprinting: application to CEST and nuclear Overhauser enhancement imaging. Magn. Reson. Med. 85, 2040–2054 (2021).

    Article  PubMed  Google Scholar 

  42. Cohen, O. et al. CEST MR fingerprinting (CEST–MRF) for brain tumor quantification using EPI readout and deep learning reconstruction. Magn. Reson. Med. 89, 233–249 (2023).

    Article  PubMed  Google Scholar 

  43. Weigand-Whittier, J. et al. Accelerated and quantitative three-dimensional molecular MRI using a generative adversarial network. Magn. Reson. Med. 89, 1901–1914 (2023).

    Article  CAS  PubMed  Google Scholar 

  44. Singh, M. et al. Bloch simulator–driven deep recurrent neural network for magnetization transfer contrast MR fingerprinting and CEST imaging. Magn. Reson. Med. 90, 1518–1536 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Kang, B., Singh, M., Park, H. & Heo, H.-Y. Only-train-once MR fingerprinting for B0 and B1 inhomogeneity correction in quantitative magnetization-transfer contrast. Magn. Reson. Med. 90, 90–102 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Perlman, O. & Azhari, H. in Nanotechnology Characterization Tools for Biosensing and Medical Diagnosis (ed. Kumar, C. S. S. R.) 333–365 (Springer, 2018).

  47. James, M. L. & Gambhir, S. S. A molecular imaging primer: modalities, imaging agents, and applications. Physiol. Rev. 92, 897–965 (2012).

    Article  CAS  PubMed  Google Scholar 

  48. Vladimirov, N. & Perlman, O. Molecular MRI-based monitoring of cancer immunotherapy treatment response. Int. J. Mol. Sci. 24, 3151 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Rowe, S. P. & Pomper, M. G. Molecular imaging in oncology: current impact and future directions. CA Cancer J. Clin. 72, 333–352 (2021).

    PubMed  PubMed Central  Google Scholar 

  50. Woessner, D. E., Zhang, S., Merritt, M. E. & Sherry, A. D. Numerical solution of the Bloch equations provides insights into the optimum design of PARACEST agents for MRI. Magn. Reson. Med. 53, 790–799 (2005).

    Article  CAS  PubMed  Google Scholar 

  51. Zhou, J. et al. Quantitative description of proton exchange processes between water and endogenous and exogenous agents for WEX, CEST, and APT experiments. Magn. Reson. Med. 51, 945–952 (2004).

    Article  PubMed  Google Scholar 

  52. Ji, Y. et al. Progress toward quantitative in vivo chemical exchange saturation transfer (CEST) MRI. Isr. J. Chem. 57, 809–824 (2017).

    Article  CAS  Google Scholar 

  53. Kim, J., Wu, Y., Guo, Y., Zheng, H. & Sun, P. Z. A review of optimization and quantification techniques for chemical exchange saturation transfer MRI toward sensitive in vivo imaging. Contrast Media Mol. Imaging 10, 163–178 (2015).

    Article  CAS  PubMed  Google Scholar 

  54. Ward, K. M. & Balaban, R. S. Determination of pH using water protons and chemical exchange dependent saturation transfer (CEST). Magn. Reson. Med. 44, 799–802 (2000).

    Article  CAS  PubMed  Google Scholar 

  55. Ji, Y. et al. In vivo pH mapping with omega plot‐based quantitative chemical exchange saturation transfer MRI. Magn. Reson. Med. 89, 299–307 (2023).

    Article  CAS  PubMed  Google Scholar 

  56. Wu, R. et al. Quantitative chemical exchange saturation transfer (qCEST) MRI–omega plot analysis of RF‐spillover‐corrected inverse CEST ratio asymmetry for simultaneous determination of labile proton ratio and exchange rate. NMR Biomed. 28, 376–383 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Perlman, O., Farrar, C. T. & Heo, H.-Y. MR fingerprinting for semisolid magnetization transfer and chemical exchange saturation transfer quantification. NMR Biomed. 36, e4710 (2023).

    Article  PubMed  Google Scholar 

  58. Heo, H.-Y. et al. Quantitative assessment of amide proton transfer (APT) and nuclear Overhauser enhancement (NOE) imaging with extrapolated semi-solid magnetization transfer reference (EMR) signals: application to a rat glioma model at 4.7 Tesla. Magn. Reson. Med. 75, 137–149 (2016).

    Article  CAS  PubMed  Google Scholar 

  59. McMahon, M. T. et al. Quantifying exchange rates in chemical exchange saturation transfer agents using the saturation time and saturation power dependencies of the magnetization transfer effect on the magnetic resonance imaging signal (QUEST and QUESP): pH calibration for poly‐l‐lysine and a starburst dendrimer. Magn. Reson. Med. 55, 836–847 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Zaiss, M. et al. QUESP and QUEST revisited–fast and accurate quantitative CEST experiments. Magn. Reson. Med. 79, 1708–1721 (2018).

    Article  CAS  PubMed  Google Scholar 

  61. Zaiß, M., Schmitt, B. & Bachert, P. Quantitative separation of CEST effect from magnetization transfer and spillover effects by Lorentzian-line-fit analysis of z-spectra. J. Magn. Reson. 211, 149–155 (2011).

    Article  PubMed  Google Scholar 

  62. Zhou, I. et al. Quantitative chemical exchange saturation transfer (CEST) MRI of glioma using Image Downsampling Expedited Adaptive Least-squares (IDEAL) fitting. Sci. Rep. 7, 84 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Roeloffs, V., Meyer, C., Bachert, P. & Zaiss, M. Towards quantification of pulsed spinlock and CEST at clinical MR scanners: an analytical interleaved saturation–relaxation (ISAR) approach. NMR Biomed. 28, 40–53 (2014).

    Article  PubMed  Google Scholar 

  64. Perlman, O., Zhu, B., Zaiss, M., Rosen, M. S. & Farrar, C. T. An end-to-end AI-based framework for automated discovery of rapid CEST/MT MRI acquisition protocols and molecular parameter quantification (AutoCEST). Magn. Reson. Med. 87, 2792–2810 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Perlman, O. et al. CEST MR-fingerprinting: practical considerations and insights for acquisition schedule design and improved reconstruction. Magn. Reson. Med. 83, 462–478 (2020).

    Article  PubMed  Google Scholar 

  66. Jeffrey, I. W., Bushell, M., Tilleray, V. J., Morley, S. & Clemens, M. J. Inhibition of protein synthesis in apoptosis: differential requirements by the tumor necrosis factor α family and a DNA-damaging agent for caspases and the double-stranded RNA-dependent protein kinase. Cancer Res. 62, 2272–2280 (2002).

    CAS  PubMed  Google Scholar 

  67. Chen, L. et al. In vivo imaging of phosphocreatine with artificial neural networks. Nat. Commun. 11, 1072 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  68. Anemone, A., Consolino, L. & Longo, D. L. MRI–CEST assessment of tumour perfusion using X-ray iodinated agents: comparison with a conventional Gd-based agent. Eur. Radiol. 27, 2170–2179 (2017).

    Article  PubMed  Google Scholar 

  69. Zaiss, M., Kunz, P., Goerke, S., Radbruch, A. & Bachert, P. MR imaging of protein folding in vitro employing nuclear-Overhauser-mediated saturation transfer. NMR Biomed. 26, 1815–1822 (2013).

    Article  CAS  PubMed  Google Scholar 

  70. Goerke, S. et al. Aggregation-induced changes in the chemical exchange saturation transfer (CEST) signals of proteins. NMR Biomed. 30, e3665 (2017).

    Article  Google Scholar 

  71. Zhou, Y. et al. Magnetic resonance imaging of glycogen using its magnetic coupling with water. Proc. Natl Acad. Sci. USA 117, 3144–3149 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Zaiss, M. et al. Relaxation-compensated CEST–MRI of the human brain at 7 T: unbiased insight into NOE and amide signal changes in human glioblastoma. Neuroimage 112, 180–188 (2015).

    Article  PubMed  Google Scholar 

  73. Layton, K. J. et al. Pulseq: a rapid and hardware-independent pulse sequence prototyping framework. Magn. Reson. Med. 77, 1544–1552 (2017).

    Article  CAS  PubMed  Google Scholar 

  74. Herz, K. et al. Pulseq-CEST: towards multi-site multi-vendor compatibility and reproducibility of CEST experiments using an open-source sequence standard. Magn. Reson. Med. 86, 1845–1858 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Roos, T. H. M. et al. Open-source Pulseq sequences on Philips MRI scanners. Preprint at http://arxiv.org/abs/2310.06962 (2023).

  76. Kogan, F. et al. In vivo chemical exchange saturation transfer imaging of creatine (CrCEST) in skeletal muscle at 3T. J. Magn. Reson. Imaging 40, 596–602 (2014).

    Article  PubMed  Google Scholar 

  77. Wu, B. et al. An overview of CEST MRI for non-MR physicists. EJNMMI Phys. 3, 1–21 (2016).

    Article  Google Scholar 

  78. Khlebnikov, V., van der Kemp, W. J., Hoogduin, H., Klomp, D. W. & Prompers, J. J. Analysis of chemical exchange saturation transfer contributions from brain metabolites to the Z-spectra at various field strengths and pH. Sci. Rep. 9, 1089 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  79. Vinogradov, E., Sherry, A. D. & Lenkinski, R. E. CEST: from basic principles to applications, challenges and opportunities. J. Magn. Reson. 229, 155–172 (2013).

    Article  CAS  PubMed  Google Scholar 

  80. Liu, G., Gilad, A. A., Bulte, J. W., Van Zijl, P. C. & McMahon, M. T. High-throughput screening of chemical exchange saturation transfer MR contrast agents. Contrast Media Mol. Imaging 5, 162–170 (2010).

    Article  CAS  PubMed  Google Scholar 

  81. Yao, J. et al. A physical phantom for amine chemical exchange saturation transfer (CEST) MRI. Magn. Reson. Mater. Phys. Biol. Med. 34, 569–580 (2021).

    Article  CAS  Google Scholar 

  82. Cember, A. T., Nanga, R. P. R. & Reddy, R. Glutamate-weighted CEST (gluCEST) imaging for mapping neurometabolism: An update on the state of the art and emerging findings from in vivo applications. NMR Biomed. 36, e4780 (2023).

    Article  CAS  PubMed  Google Scholar 

  83. Zaiss, M., Jin, T., Kim, S.-G. & Gochberg, D. F. Theory of chemical exchange saturation transfer MRI in the context of different magnetic fields. NMR Biomed. 35, e4789 (2022).

    Article  CAS  PubMed  Google Scholar 

  84. Ladd, M. E. et al. Pros and cons of ultra-high-field MRI/MRS for human application. Prog. Nuclear Magn. Reson. Spectrosc. 109, 1–50 (2018).

    Article  CAS  Google Scholar 

  85. Van Zijl, P. C., Lam, W. W., Xu, J., Knutsson, L. & Stanisz, G. J. Magnetization transfer contrast and chemical exchange saturation transfer MRI. Features and analysis of the field-dependent saturation spectrum. Neuroimage 168, 222–241 (2018).

    Article  PubMed  Google Scholar 

  86. Cohen, O. & Rosen, M. S. Algorithm comparison for schedule optimization in MR fingerprinting. Magn. Reson. Imaging 41, 15–21 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  87. Zhao, B. et al. Optimal experiment design for magnetic resonance fingerprinting: Cramér-Rao bound meets spin dynamics. IEEE Trans. Med. Imaging 38, 844–861 (2018).

    Article  PubMed Central  Google Scholar 

  88. Sommer, K. et al. Towards predicting the encoding capability of MR fingerprinting sequences. Magn. Reson. Imaging 41, 7–14 (2017).

    Article  CAS  PubMed  Google Scholar 

  89. Kara, D. et al. Parameter map error due to normal noise and aliasing artifacts in MR fingerprinting. Magn. Reson. Med. 81, 3108–3123 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Cohen, O. & Otazo, R. Global deep learning optimization of chemical exchange saturation transfer magnetic resonance fingerprinting acquisition schedule. NMR Biomed. 36, e4954 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Heo, H.-Y., Singh, M., Yedavalli, V., Jiang, S. & Zhou, J. CEST and nuclear Overhauser enhancement imaging with deep learning–extrapolated semisolid magnetization transfer reference: Scan-rescan reproducibility and reliability studies. Magn. Reson. Med. 91, 1002–1015 (2024).

    Article  PubMed  Google Scholar 

  92. Heo, H.-Y. et al. Prospective acceleration of parallel RF transmission-based 3D chemical exchange saturation transfer imaging with compressed sensing. Magn. Reson. Med. 82, 1812–1821 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Mueller, S. et al. Whole brain snapshot CEST at 3T using 3D-EPI: aiming for speed, volume, and homogeneity. Magn. Reson. Med. 84, 2469–2483 (2020).

    Article  PubMed  Google Scholar 

  94. Zaiss, M., Ehses, P. & Scheffler, K. Snapshot-CEST: optimizing spiral-centric-reordered gradient echo acquisition for fast and robust 3D CEST MRI at 9.4 T. NMR Biomed. 31, e3879 (2018).

    Article  PubMed  Google Scholar 

  95. Liu, G., Song, X., Chan, K. W. & McMahon, M. T. Nuts and bolts of CEST MR imaging. NMR Biomed. 26, 810 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  96. Liu, J. et al. Encoding capability prediction of acquisition schedules in CEST MR fingerprinting for pH quantification. Magn. Reson. Med. 87, 2044–2052 (2022).

    Article  PubMed  Google Scholar 

  97. Kang, B., Kim, B., Park, H. & Heo, H.-Y. Learning-based optimization of acquisition schedule for magnetization transfer contrast MR fingerprinting. NMR Biomed. 35, e4662 (2022).

    Article  PubMed  Google Scholar 

  98. McConnell, H. M. Reaction rates by nuclear magnetic resonance. J. Chem. Phys. 28, 430–431 (1958).

    Article  CAS  Google Scholar 

  99. Zaiss, M. et al. A combined analytical solution for chemical exchange saturation transfer and semi-solid magnetization transfer. NMR Biomed. 28, 217–230 (2015).

    Article  CAS  PubMed  Google Scholar 

  100. Golub, G. H. & Van Loan, C. F. Matrix Computations (Johns Hopkins Univ. Press, 2013).

  101. Van Zijl, P. C. et al. Mechanism of magnetization transfer during on-resonance water saturation. A new approach to detect mobile proteins, peptides, and lipids. Magn. Reson. Med. 49, 440–449 (2003).

    Article  PubMed  Google Scholar 

  102. Stanisz, G. J. et al. T1, T2 relaxation and magnetization transfer in tissue at 3T. Magn. Reson. Med. 54, 507–512 (2005).

    Article  PubMed  Google Scholar 

  103. Geades, N. et al. Quantitative analysis of the z-spectrum using a numerically simulated look-up table: application to the healthy human brain at 7T. Magn. Reson. Med. 78, 645–655 (2017).

    Article  CAS  PubMed  Google Scholar 

  104. Liu, D. et al. Quantitative characterization of nuclear overhauser enhancement and amide proton transfer effects in the human brain at 7 tesla. Magn. Reson. Med. 70, 1070–1081 (2013).

    Article  PubMed  Google Scholar 

  105. Yarnykh, V. L. et al. Fast whole-brain three-dimensional macromolecular proton fraction mapping in multiple sclerosis. Radiology 274, 210–220 (2015).

    Article  PubMed  Google Scholar 

  106. Samsonov, A. et al. Quantitative MR imaging of two-pool magnetization transfer model parameters in myelin mutant shaking pup. Neuroimage 62, 1390–1398 (2012).

    Article  PubMed  Google Scholar 

  107. Xu, J., Chung, J. J. & Jin, T. Chemical exchange saturation transfer imaging of creatine, phosphocreatine, and protein arginine residue in tissues. NMR Biomed. 36, e4671 (2023).

    Article  CAS  PubMed  Google Scholar 

  108. Kazemi, K. & Noorizadeh, N. Quantitative comparison of SPM, FSL, and brainsuite for brain MR image segmentation. J. Biomed. Phys. Eng. 4, 13 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Glang, F. et al. DeepCEST 3T: robust MRI parameter determination and uncertainty quantifcation with neural networks—application to CEST imaging of the human brain at 3T. Magn. Reson. Med. 84, 450–466 (2020).

    Article  PubMed  Google Scholar 

  110. Assländer, J. et al. Rapid quantitative magnetization transfer imaging: utilizing the hybrid state and the generalized Bloch model. Magn. Reson. Med. 91, 1478–1497 (2024).

    Article  PubMed  Google Scholar 

  111. Nagar, D., Vladimirov, N., Farrar, C. T. & Perlman, O. Dynamic and rapid deep synthesis of chemical exchange saturation transfer and semisolid magnetization transfer MRI signals. Sci. Rep. 13, 18291 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Heo, H. Y. et al. Unraveling contributions to the Z‐spectrum signal at 3.5 ppm of human brain tumors. Magn. Reson. Med. 92, 2641–2651 (2024).

    CAS  PubMed  Google Scholar 

  113. Zaiss, M. et al. Downfield-NOE-suppressed amide-CEST–MRI at 7 Tesla provides a unique contrast in human glioblastoma. Magn. Reson. Med. 77, 196–208 (2017).

    Article  CAS  PubMed  Google Scholar 

  114. Cohen-Adad, J. et al. Generic acquisition protocol for quantitative MRI of the spinal cord. Nat. Protocols 16, 4611–4632 (2021).

    Article  CAS  PubMed  Google Scholar 

  115. Bar-Shir, A., Liu, G., Greenberg, M. M., Bulte, J. W. & Gilad, A. A. Synthesis of a probe for monitoring HSV1-tk reporter gene expression using chemical exchange saturation transfer MRI. Nat. Protocols 8, 2380–2391 (2013).

    Article  CAS  PubMed  Google Scholar 

  116. Krupnick, A. S. et al. Quantitative monitoring of mouse lung tumors by magnetic resonance imaging. Nat. Protocols 7, 128–142 (2012).

    Article  CAS  PubMed  Google Scholar 

  117. Kim, M., Gillen, J., Landman, B. A., Zhou, J. & Van Zijl, P. C. Water saturation shift referencing (WASSR) for chemical exchange saturation transfer (CEST) experiments. Magn. Reson. Med. 61, 1441–1450 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  118. Schuenke, P. et al. Simultaneous mapping of water shift and B1 (WASABI)—application to field-inhomogeneity correction of CEST MRI data. Magn. Reson. Med. 77, 571–580 (2017).

    Article  PubMed  Google Scholar 

  119. Zhou, J. et al. Review and consensus recommendations on clinical APT-weighted imaging approaches at 3T: application to brain tumors. Magn. Reson. Med. 88, 546–574 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  120. Sun, P. Z. Simplified quantification of labile proton concentration-weighted chemical exchange rate (kws) with RF saturation time dependent ratiometric analysis (QUESTRA): normalization of relaxation and RF irradiation spillover effects for improved quantitative chemical exchange saturation transfer (CEST) MRI. Magn. Reson. Med. 67, 936–942 (2012).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors would like to thank K. Herz for his valuable work on pulseq–CEST standard development, D. Korenchan for his work on the Paravision 360 protocol, and B. Kang, H. Shmueli and A. Finkelstein for their technical assistance and feedback. This work was supported by the Ministry of Innovation, Science and Technology, Israel, and the Tel Aviv University Center for AI and Data Science (TAD). The authors acknowledge financial support from the NIH/NIBIB grants R01EB031008, R37-CA262662 and R01EB029974. This project was funded by the European Union (ERC, BabyMagnet, project no. 101115639). Views and opinions expressed are, however, those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.

Author information

Author notes

  1. These authors contributed equally: Christian T. Farrar, Or Perlman.

Authors and Affiliations

  1. Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel

    Nikita Vladimirov & Or Perlman

  2. Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Ouri Cohen

  3. Divison of MR Research, Department of Radiology, Johns Hopkins University, Baltimore, MD, USA

    Hye-Young Heo

  4. F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA

    Hye-Young Heo

  5. Institute of Neuroradiology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany

    Moritz Zaiss

  6. Department of Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany

    Moritz Zaiss

  7. Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA

    Christian T. Farrar

  8. Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel

    Or Perlman

Authors
  1. Nikita Vladimirov
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  2. Ouri Cohen
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  5. Christian T. Farrar
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  6. Or Perlman
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Contributions

Conceptualization: N.V., C.T.F. and O.P. Methodology: N.V., O.C., H.-Y.H., M.Z., C.T.F. and O.P. Data curation: O.C., H.-Y.H., M.Z., C.T.F. and O.P. Writing: N.V., H.-Y.H., C.T.F. and O.P. Reviewing and editing: N.V., O.C., H.-Y.H., M.Z., C.T.F. and O.P. Supervision: O.P.

Corresponding author

Correspondence to Or Perlman.

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Competing interests

The authors declare the following competing interests: C.T.F. and O.C. hold a patent for the CEST–MRF method (patent no. US10,605,877).

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Nature Protocols thanks Jakob Asslander and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Key references

Perlman, O. et al. Nat. Biomed. Eng. 6, 648–657 (2022): https://doi.org/10.1038/s41551-021-00809-7

Cohen, O. et al. Magn. Reson. Med. 89, 233–249 (2023): https://doi.org/10.1002/mrm.29448

Kang, B. et al. Magn. Reson. Med. 85, 2040–2054 (2021): https://doi.org/10.1002/mrm.28573

Supplementary information

Supplementary Information

Supplementary Figs. 1 and 2, Discussion 1 and Table 1–5.

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Vladimirov, N., Cohen, O., Heo, HY. et al. Quantitative molecular imaging using deep magnetic resonance fingerprinting. Nat Protoc 20, 3024–3054 (2025). https://doi.org/10.1038/s41596-025-01152-w

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