Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2-Ex vivo imaging: Added value and acquisition

Kurt G Schilling; Francesco Grussu; Andrada Ianus; Brian Hansen; Amy F D Howard; Rachel L C Barrett; Manisha Aggarwal; Stijn Michielse; Fatima Nasrallah; Warda Syeda; Nian Wang; Jelle Veraart; Alard Roebroeck; Andrew F Bagdasarian; Cornelius Eichner; Farshid Sepehrband; Jan Zimmermann; Lucas Soustelle; Christien Bowman; Benjamin C Tendler; Andreea Hertanu; Ben Jeurissen; Marleen Verhoye; Lucio Frydman; Yohan van de Looij; David Hike; Jeff F Dunn; Karla Miller; Bennett A Landman; Noam Shemesh; Adam Anderson; Emilie McKinnon; Shawna Farquharson; Flavio Dell'Acqua; Carlo Pierpaoli; Ivana Drobnjak; Alexander Leemans; Kevin D Harkins; Maxime Descoteaux; Duan Xu; Hao Huang; Mathieu D Santin; Samuel C Grant; Andre Obenaus; Gene S Kim; Dan Wu; Denis Le Bihan; Stephen J Blackband; Luisa Ciobanu; Els Fieremans; Ruiliang Bai; Trygve B Leergaard; Jiangyang Zhang; Tim B Dyrby; G Allan Johnson; Julien Cohen-Adad; Matthew D Budde; Ileana O Jelescu

doi:10.1002/mrm.30435

Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2-Ex vivo imaging: Added value and acquisition

Magn Reson Med. 2025 Mar 4. doi: 10.1002/mrm.30435. Online ahead of print.

Authors

Kurt G Schilling^{1

2}, Francesco Grussu^{3

4}, Andrada Ianus^{5

6}, Brian Hansen⁷, Amy F D Howard^{8

9}, Rachel L C Barrett^{10

11}, Manisha Aggarwal¹², Stijn Michielse¹³, Fatima Nasrallah¹⁴, Warda Syeda¹⁵, Nian Wang^{16

17}, Jelle Veraart¹⁸, Alard Roebroeck¹⁹, Andrew F Bagdasarian^{20

21}, Cornelius Eichner²², Farshid Sepehrband²³, Jan Zimmermann²⁴, Lucas Soustelle²⁵, Christien Bowman^{26

27}, Benjamin C Tendler²⁸, Andreea Hertanu²⁹, Ben Jeurissen^{30

31}, Marleen Verhoye^{26

27}, Lucio Frydman³², Yohan van de Looij³³, David Hike^{20

21}, Jeff F Dunn^{34

35

36}, Karla Miller⁹, Bennett A Landman³⁷, Noam Shemesh⁵, Adam Anderson^{2

38}, Emilie McKinnon³⁹, Shawna Farquharson⁴⁰, Flavio Dell'Acqua⁴¹, Carlo Pierpaoli⁴², Ivana Drobnjak⁴³, Alexander Leemans⁴⁴, Kevin D Harkins^{1

2

45}, Maxime Descoteaux^{46

47}, Duan Xu⁴⁸, Hao Huang^{49

50}, Mathieu D Santin^{51

52}, Samuel C Grant^{20

21}, Andre Obenaus^{53

54}, Gene S Kim⁵⁵, Dan Wu⁵⁶, Denis Le Bihan^{57

58}, Stephen J Blackband^{59

60

61}, Luisa Ciobanu⁶², Els Fieremans⁶³, Ruiliang Bai^{64

65}, Trygve B Leergaard⁶⁶, Jiangyang Zhang⁶⁷, Tim B Dyrby^{68

69}, G Allan Johnson^{70

71}, Julien Cohen-Adad^{72

73

74}, Matthew D Budde^{75

76}, Ileana O Jelescu^{29

77}

Affiliations

¹ Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
² Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, USA.
³ Radiomics Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
⁴ Queen Square MS Centre, Queen Square Institute of Neurology, Faculty of Brain Sciences, University College London, London, UK.
⁵ Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal.
⁶ School of Biomedical Engineering and Imaging Sciences, King's College London, London.
⁷ Center of Functionally Integrative Neuroscience, Aarhus University, Aarhus, Denmark.
⁸ Department of Bioengineering, Imperial College London, London, UK.
⁹ FMRIB Centre, Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
¹⁰ Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
¹¹ NatBrainLab, Department of Forensics and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London|, London, UK.
¹² Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
¹³ Department of Neurosurgery, School for Mental Health and Neuroscience (MHeNS), Maastricht University Medical Center, Maastricht, The Netherlands.
¹⁴ The Queensland Brain Institute, The University of Queensland, Queensland, Australia.
¹⁵ Melbourne Neuropsychiatry Centre, The University of Melbourne, Parkville, Australia.
¹⁶ Department of Radiology and Imaging Sciences, Indiana University, Bloomington, Indiana, USA.
¹⁷ Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA.
¹⁸ Center for Biomedical Imaging, NYU Grossman School of Medicine, New York, New York, USA.
¹⁹ Faculty of psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands.
²⁰ Department of Chemical & Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida, USA.
²¹ Center for Interdisciplinary Magnetic Resonance, National HIgh Magnetic Field Laboratory, Tallahassee, Florida, USA.
²² Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
²³ USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA.
²⁴ Department of Neuroscience, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota, USA.
²⁵ Aix Marseille Univ, CNRS, CRMBM, Marseille, France.
²⁶ Bio-Imaging Lab, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium.
²⁷ μNEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium.
²⁸ Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
²⁹ Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
³⁰ imec Vision Lab, Dept. of Physics, University of Antwerp, Antwerp, Belgium.
³¹ Lab for Equilibrium Investigations and Aerospace, Dept. of Physics, University of Antwerp, Antwerp, Belgium.
³² Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
³³ Division of Child Development & Growth, Department of Pediatrics, Gynaecology & Obstetrics, School of Medicine, Université de Genève, Genève, Switzerland.
³⁴ Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
³⁵ Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
³⁶ Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
³⁷ Department of Electrical and Computer Engineering, Vanderbilt University.
³⁸ Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
³⁹ Medical University of South Carolina, Charleston, South Carolina, USA.
⁴⁰ National Imaging Facility, The University of Queensland, Brisbane, Australia.
⁴¹ Department of Forensic and Neurodevelopmental Sciences, King's College London, London, UK.
⁴² Laboratory on Quantitative Medical imaging, NIBIB, National Institutes of Health, Bethesda, Maryland, USA.
⁴³ Department of Computer Science, University College London, London, UK.
⁴⁴ PROVIDI Lab, Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
⁴⁵ Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA.
⁴⁶ Sherbrooke Connectivity Imaing Lab (SCIL), Computer Science department, Université de Sherbrooke, Sherbrooke, Quebec, Canada.
⁴⁷ Imeka Solutions, Sherbrooke, Quebec, Canada.
⁴⁸ Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA.
⁴⁹ Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
⁵⁰ Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
⁵¹ Centre for NeuroImaging Research (CENIR), Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Paris, France.
⁵² Paris Brain Institute, Paris, France.
⁵³ Department of Pediatrics, University of California Irvine, Irvine, California, USA.
⁵⁴ Preclinical and Translational Imaging Center, University of California Irvine, Irvine, California, USA.
⁵⁵ Department of Radiology, Weill Cornell Medical College, New York, New York, USA.
⁵⁶ Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China.
⁵⁷ CEA, DRF, JOLIOT, NeuroSpin, Gif-sur-Yvette, France.
⁵⁸ Université Paris-Saclay, Gif-sur-Yvette, France.
⁵⁹ Department of Neuroscience, University of Florida, Gainesville, Florida, USA.
⁶⁰ McKnight Brain Institute, University of Florida, Gainesville, Florida, USA.
⁶¹ National High Magnetic Field Laboratory, Tallahassee, Florida, USA.
⁶² NeuroSpin, UMR CEA/CNRS 9027, Paris-Saclay University, Gif-sur-Yvette, France.
⁶³ Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA.
⁶⁴ Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, China.
⁶⁵ Frontier Center of Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China.
⁶⁶ Department of Molecular Biology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
⁶⁷ Department of Radiology, New York University School of Medicine, New York, New York, USA.
⁶⁸ Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager & Hvidovre, Hvidovre, Denmark.
⁶⁹ Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.
⁷⁰ Duke Center for In Vivo Microscopy, Department of Radiology, Duke University, Durham, North Carolina, USA.
⁷¹ Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.
⁷² NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Quebec, Canada.
⁷³ Functional Neuroimaging Unit, CRIUGM, University of Montreal, Montreal, Quebec, Canada.
⁷⁴ Mila - Quebec AI Institute, Montreal, Quebec, Canada.
⁷⁵ Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
⁷⁶ Clement J Zablocki VA Medical Center, Milwaukee, Wisconsin, USA.
⁷⁷ CIBM Center for Biomedical Imaging, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

PMID: 40035293
DOI: 10.1002/mrm.30435

Abstract

The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher SNR and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts for improved microstructure and connectivity characterization. Another major advantage of ex vivo dMRI is the direct comparison with histological data, as a crucial methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work represents "Part 2" of a three-part series of recommendations and considerations for preclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with a focus on the value that ex vivo imaging adds to the field of dMRI and considerations in ex vivo image acquisition. We first give general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in specimens and models and discuss why some may be more or less appropriate for different studies. We then give guidelines for ex vivo protocols, including tissue fixation, sample preparation, and MR scanning. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. An overarching goal herein is to enhance the rigor and reproducibility of ex vivo dMRI acquisitions and analyses, and thereby advance biomedical knowledge.

Keywords: acquisition; best practices; diffusion MRI; diffusion tensor; ex vivo; microstructure; open science; preclinical; processing; tractography.

Abstract

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