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

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Title: Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2—Ex vivo imaging: Added value and acquisition: Part 2—Ex vivo imaging: Added value and acquisition
Authors: Schilling, Kurt G., Grussu, Francesco, Ianus, Andrada, Hansen, Brian, Howard, Amy F. D., Barrett, Rachel L. C., Aggarwal, Manisha, Michielse, Stijn, Nasrallah, Fatima, Syeda, Warda, Wang, Nian, Veraart, Jelle, Roebroeck, Alard, Bagdasarian, Andrew F., Eichner, Cornelius, Sepehrband, Farshid, Zimmermann, Jan, Soustelle, Lucas, Bowman, Christien, Tendler, Benjamin C., Hertanu, Andreea, Jeurissen, Ben, Verhoye, Marleen, Frydman, Lucio, van de Looij, Yohan, Hike, David, Dunn, Jeff F., Miller, Karla, Landman, Bennett A., Shemesh, Noam, Anderson, Adam, McKinnon, Emilie, Farquharson, Shawna, Dell'Acqua, Flavio, Pierpaoli, Carlo, Drobnjak, Ivana, Leemans, Alexander, Harkins, Kevin D., Descoteaux, Maxime, Xu, Duan, Huang, Hao, Santin, Mathieu D., Grant, Samuel C., Obenaus, Andre, Kim, Gene S., Wu, Dan, Le Bihan, Denis, Blackband, Stephen J., Ciobanu, Luisa, Fieremans, Els, Bai, Ruiliang, Leergaard, Trygve B., Zhang, Jiangyang, Dyrby, Tim B., Johnson, G. Allan, Cohen‐Adad, Julien, Budde, Matthew D., Jelescu, Ileana O.
Contributors: Institut Català de la Salut, [Schilling KG] Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee USA. Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee USA. [Grussu F] Radiomics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain. Queen Square MS Centre, Queen Square Institute of Neurology, Faculty of Brain Sciences, University College London, London, UK. [Ianus A] Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal. School of Biomedical Engineering and Imaging Sciences, King’s College London, London. [Hansen B] Center of Functionally Integrative Neuroscience, Aarhus University, Aarhus, Denmark. [Howard AFD] Department of Bioengineering, Imperial College London, London, UK. FMRIB Centre, Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK. [Barrett RLC] Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK. NatBrainLab, Department of Forensics and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK, Vall d'Hebron Barcelona Hospital Campus, Beeldverwerking ISI, Brain, Cancer
Source: Magn Reson Med
Scientia
Scientia. Dipòsit d'Informació Digital del Departament de Salut
instname
Magnetic resonance in medicine, vol. 93, no. 6, pp. 2535-2560
Magnetic resonance in medicine
Schilling, K G, Grussu, F, Ianus, A, Hansen, B, Howard, A FD, Barrett, R L C, Aggarwal, M, Michielse, S, Nasrallah, F, Syeda, W, Wang, N, Veraart, J, Roebroeck, A, Bagdasarian, A F, Eichner, C, Sepehrband, F, Zimmermann, J, Soustelle, L, Bowman, C, Tendler, B C, Hertanu, A, Jeurissen, B, Frydman, L, van de Looij, Y, Hike, D, Dunn, J F, Miller, K, Landman, B A, Shemesh, N, Anderson, A, McKinnon, E, Farquharson, S, Acqua, F D, Pierpaoli, C, Drobnjak, I, Leemans, A, Harkins, K D, Descoteaux, M, Xu, D, Huang, H, Santin, M D, Grant, S C, Obenaus, A, Kim, G S, Wu, D, Bihan, D L, Blackband, S J, Ciobanu, L, Fieremans, E, Bai, R, Leergaard, T, Zhang, J, Dyrby, T B, Johnson, G A, Cohen-Adad, J, Budde, M D & Jelescu, I O 2025, 'Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI : Part 2--Ex vivo imaging: added value and acquisition', Magnetic Resonance in Medicine, vol. 93, no. 6, pp. 2535-2560. https://doi.org/10.1002/mrm.30435
Schilling, K G, Grussu, F, Ianus, A, Hansen, B, Howard, A F D, Barrett, R L C, Aggarwal, M, Michielse, S, Nasrallah, F, Syeda, W, Wang, N, Veraart, J, Roebroeck, A, Bagdasarian, A F, Eichner, C, Sepehrband, F, Zimmermann, J, Soustelle, L, Bowman, C, Tendler, B C, Hertanu, A, Jeurissen, B, Verhoye, M, Frydman, L, van de Looij, Y, Hike, D, Dunn, J F, Miller, K, Landman, B A, Shemesh, N, Anderson, A, McKinnon, E, Farquharson, S, Dell'Acqua, F, Pierpaoli, C, Drobnjak, I, Leemans, A, Harkins, K D, Descoteaux, M, Xu, D, Huang, H, Santin, M D, Grant, S C, Obenaus, A, Kim, G S, Wu, D, Le Bihan, D, Blackband, S J, Ciobanu, L, Fieremans, E, Bai, R, Leergaard, T B, Zhang, J, Dyrby, T B, Johnson, G A, Cohen-Adad, J, Budde, M D & Jelescu, I O 2025, 'Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI : Part 2-Ex vivo imaging: Added value and acquisition', Magnetic Resonance in Medicine, vol. 93, no. 6, pp. 2535-2560. https://doi.org/10.1002/mrm.30435
Publication Status: Preprint
Publisher Information: Wiley, 2025.
Publication Year: 2025
Subject Terms: q-bio.TO, TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::diagnóstico::técnicas y procedimientos diagnósticos::diagnóstico por imagen::tomografía::imagen por resonancia magnética::imagen de resonancia magnética de difusión, tractography, Review, physics.med-ph, Signal-To-Noise Ratio, Diffusion Magnetic Resonance Imaging/methods, Brain/diagnostic imaging, Animals, Image Processing, Computer-Assisted/methods, Humans, Reproducibility of Results, acquisition, best practices, diffusion MRI, diffusion tensor, ex vivo, microstructure, open science, preclinical, processing, 0302 clinical medicine, TENSOR MICROSCOPY, Image Processing, Computer-Assisted, ANATOMÍA::sistema nervioso::sistema nervioso central::encéfalo, Tissues and Organs (q-bio.TO), IN-VIVO, T-2 RELAXATION, MOUSE-BRAIN, Preclinical and Clinical Imaging, Animals de laboratori, Otros calificadores::Otros calificadores::Otros calificadores::/diagnóstico por imagen, Other subheadings::Other subheadings::Other subheadings::/diagnostic imaging, Brain, WATER DIFFUSION, ORGANISMOS::Eukaryota::animales, ANATOMY::Nervous System::Central Nervous System::Brain, AXON DIAMETER, WHITE-MATTER, FOS: Physical sciences, WAXHOLM SPACE ATLAS, 03 medical and health sciences, MAGNETIC-RESONANCE MICROSCOPY, Imatges - Processament, ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Diagnosis::Diagnostic Techniques and Procedures::Diagnostic Imaging::Tomography::Magnetic Resonance Imaging::Diffusion Magnetic Resonance Imaging, Journal Article, POSTMORTEM HUMAN BRAINS, Computer. Automation, ORGANISMS::Eukaryota::Animals, INFORMATION SCIENCE::Information Science::Computing Methodologies::Image Processing, Computer-Assisted, Quantitative Biology - Tissues and Organs, Cervell - Imatgeria, Physics - Medical Physics, CIENCIA DE LA INFORMACIÓN::Ciencias de la información::metodologías computacionales::procesamiento de imágenes asistido por ordenador, Diffusion Magnetic Resonance Imaging, FOS: Biological sciences, Imatgeria per ressonància magnètica, Human medicine, Medical Physics (physics.med-ph)
Description: 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.
Document Type: Article
Other literature type
File Description: application/pdf
Language: English
ISSN: 1522-2594
0740-3194
DOI: 10.1002/mrm.30435
DOI: 10.48550/arxiv.2209.13371
Access URL: https://pubmed.ncbi.nlm.nih.gov/40035293
http://arxiv.org/abs/2209.13371
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https://doi.org/10.1002/mrm.30435
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  Data: Magn Reson Med<br />Scientia<br />Scientia. Dipòsit d'Informació Digital del Departament de Salut<br />instname<br />Magnetic resonance in medicine, vol. 93, no. 6, pp. 2535-2560<br />Magnetic resonance in medicine<br />Schilling, K G, Grussu, F, Ianus, A, Hansen, B, Howard, A FD, Barrett, R L C, Aggarwal, M, Michielse, S, Nasrallah, F, Syeda, W, Wang, N, Veraart, J, Roebroeck, A, Bagdasarian, A F, Eichner, C, Sepehrband, F, Zimmermann, J, Soustelle, L, Bowman, C, Tendler, B C, Hertanu, A, Jeurissen, B, Frydman, L, van de Looij, Y, Hike, D, Dunn, J F, Miller, K, Landman, B A, Shemesh, N, Anderson, A, McKinnon, E, Farquharson, S, Acqua, F D, Pierpaoli, C, Drobnjak, I, Leemans, A, Harkins, K D, Descoteaux, M, Xu, D, Huang, H, Santin, M D, Grant, S C, Obenaus, A, Kim, G S, Wu, D, Bihan, D L, Blackband, S J, Ciobanu, L, Fieremans, E, Bai, R, Leergaard, T, Zhang, J, Dyrby, T B, Johnson, G A, Cohen-Adad, J, Budde, M D & Jelescu, I O 2025, 'Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI : Part 2--Ex vivo imaging: added value and acquisition', Magnetic Resonance in Medicine, vol. 93, no. 6, pp. 2535-2560. https://doi.org/10.1002/mrm.30435<br />Schilling, K G, Grussu, F, Ianus, A, Hansen, B, Howard, A F D, Barrett, R L C, Aggarwal, M, Michielse, S, Nasrallah, F, Syeda, W, Wang, N, Veraart, J, Roebroeck, A, Bagdasarian, A F, Eichner, C, Sepehrband, F, Zimmermann, J, Soustelle, L, Bowman, C, Tendler, B C, Hertanu, A, Jeurissen, B, Verhoye, M, Frydman, L, van de Looij, Y, Hike, D, Dunn, J F, Miller, K, Landman, B A, Shemesh, N, Anderson, A, McKinnon, E, Farquharson, S, Dell'Acqua, F, Pierpaoli, C, Drobnjak, I, Leemans, A, Harkins, K D, Descoteaux, M, Xu, D, Huang, H, Santin, M D, Grant, S C, Obenaus, A, Kim, G S, Wu, D, Le Bihan, D, Blackband, S J, Ciobanu, L, Fieremans, E, Bai, R, Leergaard, T B, Zhang, J, Dyrby, T B, Johnson, G A, Cohen-Adad, J, Budde, M D & Jelescu, I O 2025, 'Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI : Part 2-Ex vivo imaging: Added value and acquisition', Magnetic Resonance in Medicine, vol. 93, no. 6, pp. 2535-2560. https://doi.org/10.1002/mrm.30435
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– Name: Abstract
  Label: Description
  Group: Ab
  Data: 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.
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– Name: Language
  Label: Language
  Group: Lang
  Data: English
– Name: ISSN
  Label: ISSN
  Group: ISSN
  Data: 1522-2594<br />0740-3194
– Name: DOI
  Label: DOI
  Group: ID
  Data: 10.1002/mrm.30435
– Name: DOI
  Label: DOI
  Group: ID
  Data: 10.48550/arxiv.2209.13371
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  Label: Access URL
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  Data: CC BY
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        Value: 10.1002/mrm.30435
    Languages:
      – Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 26
        StartPage: 2535
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      – SubjectFull: q-bio.TO
        Type: general
      – SubjectFull: TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::diagnóstico::técnicas y procedimientos diagnósticos::diagnóstico por imagen::tomografía::imagen por resonancia magnética::imagen de resonancia magnética de difusión
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      – SubjectFull: tractography
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      – SubjectFull: Review
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      – SubjectFull: physics.med-ph
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      – SubjectFull: Signal-To-Noise Ratio
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      – SubjectFull: Diffusion Magnetic Resonance Imaging/methods
        Type: general
      – SubjectFull: Brain/diagnostic imaging
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      – SubjectFull: Animals
        Type: general
      – SubjectFull: Image Processing, Computer-Assisted/methods
        Type: general
      – SubjectFull: Humans
        Type: general
      – SubjectFull: Reproducibility of Results
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      – SubjectFull: acquisition
        Type: general
      – SubjectFull: best practices
        Type: general
      – SubjectFull: diffusion MRI
        Type: general
      – SubjectFull: diffusion tensor
        Type: general
      – SubjectFull: ex vivo
        Type: general
      – SubjectFull: microstructure
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      – SubjectFull: open science
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      – SubjectFull: preclinical
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      – SubjectFull: processing
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      – SubjectFull: 0302 clinical medicine
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      – SubjectFull: TENSOR MICROSCOPY
        Type: general
      – SubjectFull: Image Processing, Computer-Assisted
        Type: general
      – SubjectFull: ANATOMÍA::sistema nervioso::sistema nervioso central::encéfalo
        Type: general
      – SubjectFull: Tissues and Organs (q-bio.TO)
        Type: general
      – SubjectFull: IN-VIVO
        Type: general
      – SubjectFull: T-2 RELAXATION
        Type: general
      – SubjectFull: MOUSE-BRAIN
        Type: general
      – SubjectFull: Preclinical and Clinical Imaging
        Type: general
      – SubjectFull: Animals de laboratori
        Type: general
      – SubjectFull: Otros calificadores::Otros calificadores::Otros calificadores::/diagnóstico por imagen
        Type: general
      – SubjectFull: Other subheadings::Other subheadings::Other subheadings::/diagnostic imaging
        Type: general
      – SubjectFull: Brain
        Type: general
      – SubjectFull: WATER DIFFUSION
        Type: general
      – SubjectFull: ORGANISMOS::Eukaryota::animales
        Type: general
      – SubjectFull: ANATOMY::Nervous System::Central Nervous System::Brain
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      – SubjectFull: AXON DIAMETER
        Type: general
      – SubjectFull: WHITE-MATTER
        Type: general
      – SubjectFull: FOS: Physical sciences
        Type: general
      – SubjectFull: WAXHOLM SPACE ATLAS
        Type: general
      – SubjectFull: 03 medical and health sciences
        Type: general
      – SubjectFull: MAGNETIC-RESONANCE MICROSCOPY
        Type: general
      – SubjectFull: Imatges - Processament
        Type: general
      – SubjectFull: ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Diagnosis::Diagnostic Techniques and Procedures::Diagnostic Imaging::Tomography::Magnetic Resonance Imaging::Diffusion Magnetic Resonance Imaging
        Type: general
      – SubjectFull: Journal Article
        Type: general
      – SubjectFull: POSTMORTEM HUMAN BRAINS
        Type: general
      – SubjectFull: Computer. Automation
        Type: general
      – SubjectFull: ORGANISMS::Eukaryota::Animals
        Type: general
      – SubjectFull: INFORMATION SCIENCE::Information Science::Computing Methodologies::Image Processing, Computer-Assisted
        Type: general
      – SubjectFull: Quantitative Biology - Tissues and Organs
        Type: general
      – SubjectFull: Cervell - Imatgeria
        Type: general
      – SubjectFull: Physics - Medical Physics
        Type: general
      – SubjectFull: CIENCIA DE LA INFORMACIÓN::Ciencias de la información::metodologías computacionales::procesamiento de imágenes asistido por ordenador
        Type: general
      – SubjectFull: Diffusion Magnetic Resonance Imaging
        Type: general
      – SubjectFull: FOS: Biological sciences
        Type: general
      – SubjectFull: Imatgeria per ressonància magnètica
        Type: general
      – SubjectFull: Human medicine
        Type: general
      – SubjectFull: Medical Physics (physics.med-ph)
        Type: general
    Titles:
      – TitleFull: Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2—Ex vivo imaging: Added value and acquisition: Part 2—Ex vivo imaging: Added value and acquisition
        Type: main
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            NameFull: Schilling, Kurt G.
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              Type: published
              Y: 2025
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          Titles:
            – TitleFull: Magnetic Resonance in Medicine
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