Peer-Reviewed Publication
Magn Reson Med2025;93(6):2561-2582.June 1, 2025Journal Article
Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3-Ex vivo imaging: Data processing, comparisons with microscopy, and tractography.
Kurt G Schilling1,2, Amy F D Howard3,4, Francesco Grussu5,6, Andrada Ianus7,8, Brian Hansen9, Rachel L C Barrett10,11, Manisha Aggarwal12, Stijn Michielse13, Fatima Nasrallah14, Warda Syeda15, Nian Wang16,17, Jelle Veraart18, Alard Roebroeck19, Andrew F Bagdasarian20,21, Cornelius Eichner22, Farshid Sepehrband23, Jan Zimmermann24, Lucas Soustelle25, Christien Bowman26,27, Benjamin C Tendler28, Andreea Hertanu29, Ben Jeurissen30,31, Marleen Verhoye26,27, Lucio Frydman32, Yohan van de Looij33, David Hike20,21, Jeff F Dunn34,35,36, Karla Miller4, Bennett A Landman37, Noam Shemesh8, Adam Anderson2,38, Emilie McKinnon39, Shawna Farquharson40, Flavio Dell'Acqua41, Carlo Pierpaoli42, Ivana Drobnjak43, Alexander Leemans44, Kevin D Harkins1,2,45, Maxime Descoteaux46,47, Duan Xu48, Hao Huang49,50, Mathieu D Santin51,52, Samuel C Grant20,21, Andre Obenaus53,54, Gene S Kim55, Dan Wu56, Denis Le Bihan57,58, Stephen J Blackband59,60,61, Luisa Ciobanu62, Els Fieremans63, Ruiliang Bai64,65, Trygve B Leergaard66, Jiangyang Zhang67, Tim B Dyrby68,69, G Allan Johnson70,71, Julien Cohen-Adad72,73,74, Matthew D Budde75,76, Ileana O Jelescu29,77
1Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
2Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, USA.
3Department of Bioengineering, Imperial College London, London, UK.
4FMRIB Centre, Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
5Radiomics Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
6Queen Square MS Centre, Queen Square Institute of Neurology, Faculty of Brain Sciences, University College London, London, UK.
7School of Biomedical Engineering and Imaging Sciences, King's College London, London, England.
8Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal.
9Center of Functionally Integrative Neuroscience, Aarhus University, Aarhus, Denmark.
10Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
11NatBrainLab, Department of Forensics and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
12Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
13Department of Neurosurgery, School for Mental Health and Neuroscience (MHeNS), Maastricht University Medical Center, Maastricht, The Netherlands.
14The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.
15Melbourne Neuropsychiatry Centre, The University of Melbourne, Parkville, Victoria, Australia.
16Department of Radiology and Imaging Sciences, Indiana University, Bloomington, Indiana, USA.
17Stark Neurosciences Research Institute, Indiana University School of Medicine, Bloomington, Indiana, USA.
18Center for Biomedical Imaging, NYU Grossman School of Medicine, New York, New York, USA.
19Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands.
20Department of Chemical & Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida, USA.
21Center for Interdisciplinary Magnetic Resonance, National HIgh Magnetic Field Laboratory, Tallahassee, Florida, USA.
22Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
23USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA.
24Department of Neuroscience, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota, USA.
25Aix Marseille Univ, CNRS, CRMBM, Marseille, France.
26Bio-Imaging Lab, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium.
27μNEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium.
28Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
29Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
30imec Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium.
31Lab for Equilibrium Investigations and Aerospace, Department of Physics, University of Antwerp, Antwerp, Belgium.
32Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
33Division of Child Development & Growth, Department of Pediatrics, Gynaecology & Obstetrics, School of Medicine, Université de Genève, Genève, Switzerland.
34Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
35Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
36Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
37Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, USA.
38Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
39Medical University of South Carolina, Charleston, South Carolina, USA.
40National Imaging Facility, The University of Queensland, Brisbane, Queensland, Australia.
41Department of Forensic and Neurodevelopmental Sciences, King's College London, London, UK.
42Laboratory on Quantitative Medical Imaging, NIBIB, National Institutes of Health, Bethesda, Maryland, USA.
43Department of Computer Science, University College London, London, UK.
44PROVIDI Lab, Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
45Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA.
46Sherbrooke Connectivity Imaing Lab (SCIL), Computer Science Department, Université de Sherbrooke, Sherbrooke, Quebec, Canada.
47Imeka Solutions, Sherbrooke, Quebec, Canada.
48Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA.
49Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
50Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
51Centre for NeuroImaging Research (CENIR), Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Paris, France.
52Paris Brain Institute, Paris, France.
53Department of Pediatrics, University of California Irvine, Irvine, California, USA.
54Preclinical and Translational Imaging Center, University of California Irvine, Irvine, California, USA.
55Department of Radiology, Weill Cornell Medical College, New York, New York, USA.
56Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China.
57CEA, DRF, JOLIOT, NeuroSpin, Gif-sur-Yvette, France.
58Université Paris-Saclay, Gif-sur-Yvette, France.
59Department of Neuroscience, University of Florida, Gainesville, Florida, USA.
60McKnight Brain Institute, University of Florida, Gainesville, Florida, USA.
61National High Magnetic Field Laboratory, Tallahassee, Florida, USA.
62NeuroSpin, UMR CEA/CNRS 9027, Paris-Saclay University, Gif-sur-Yvette, France.
63Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA.
64Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, China.
65Frontier Center of Brain Science and Brain-machine Integration, Zhejiang University.
66Department of Molecular Biology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
67Department of Radiology, New York University School of Medicine, New York, New York, USA.
68Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager & Hvidovre, Hvidovre, Denmark.
69Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.
70Duke Center for In Vivo Microscopy, Department of Radiology, Duke University, Durham, North Carolina, USA.
71Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.
72NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Quebec, Canada.
73Functional Neuroimaging Unit, CRIUGM, University of Montreal, Montreal, Quebec, Canada.
74Mila - Quebec AI Institute, Montreal, Quebec, Canada.
75Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
76Clement J Zablocki VA Medical Center, Milwaukee, Wisconsin, USA.
77CIBM Center for Biomedical Imaging, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
Abstract
Preclinical diffusion MRI (dMRI) has proven value in methods development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. 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 that facilitat…
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