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: Part 3-Ex vivo imaging: Data processing, comparisons with microscopy, and tractography
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| Title: | 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: Part 3-Ex vivo imaging: Data processing, comparisons with microscopy, and tractography |
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| Authors: | Kurt G. Schilling, Amy F. D. Howard, Francesco Grussu, Andrada Ianus, Brian Hansen, 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 |
| 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. [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. [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] School of Biomedical Engineering and Imaging Sciences, King’s College London, London, England. Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal. [Hansen B] Center of Functionally Integrative Neuroscience, Aarhus University, Aarhus, Denmark. [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. 2561-2582 Magnetic resonance in medicine Schilling, K G, Howard, A FD, Grussu, F, Ianus, A, Hansen, B, 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, 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 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 3--Ex vivo imaging: data processing, comparisons with microscopy, and tractography ', Magnetic Resonance in Medicine . Schilling, K G, Howard, A F D, Grussu, F, Ianus, A, Hansen, B, 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 3-Ex vivo imaging: Data processing, comparisons with microscopy, and tractography', Magnetic Resonance in Medicine, vol. 93, no. 6, pp. 2561-2582. https://doi.org/10.1002/mrm.30424 Schilling, K G, Howard, A F D, Grussu, F, Ianus, A, Hansen, B, 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 3—Ex vivo imaging: Data processing, comparisons with microscopy, and tractography', Magnetic Resonance in Medicine, vol. 93, no. 6, pp. 2561-2582. https://doi.org/10.1002/mrm.30424 |
| Publication Status: | Preprint |
| Publisher Information: | Wiley, 2025. |
| Publication Year: | 2025 |
| Subject Terms: | TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::diagnóstico::técnicas y procedimientos diagnósticos::diagnóstico por imagen::neuroimágenes::imagen con tensor de difusión, 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, TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::diagnóstico::técnicas y procedimientos diagnósticos::diagnóstico por imagen::microscopía, diffusion tensor, microstructure, tractography, FOS: Physical sciences, physics.med-ph, Signal-To-Noise Ratio, diffusion MRI, ANATOMICAL ACCURACY, 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, open science, preclinical, AXON DIAMETER DISTRIBUTION, ORIENTATION DISPERSION, Image Processing, Computer-Assisted, best practices, Animals, Humans, NERVOUS-TISSUE, Computer. Automation, Microscopy, HISTOLOGICAL VALIDATION, Diffusion Magnetic Resonance Imaging/methods, Brain/diagnostic imaging, Image Processing, Computer-Assisted/methods, Diffusion Tensor Imaging/methods, Microscopy/methods, acquisition, ex vivo, processing, Preclinical and Clinical Imaging, ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Diagnosis::Diagnostic Techniques and Procedures::Diagnostic Imaging::Neuroimaging::Diffusion Tensor Imaging, INFORMATION SCIENCE::Information Science::Computing Methodologies::Image Processing, Computer-Assisted, Brain, Physics - Medical Physics, Microscòpia clínica, CIENCIA DE LA INFORMACIÓN::Ciencias de la información::metodologías computacionales::procesamiento de imágenes asistido por ordenador, Diffusion Magnetic Resonance Imaging, Diffusion Tensor Imaging, Radiology Nuclear Medicine and imaging, ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Diagnosis::Diagnostic Techniques and Procedures::Diagnostic Imaging::Microscopy, Imatgeria per ressonància magnètica, STRUCTURE TENSOR ANALYSIS, Human medicine, Medical Physics (physics.med-ph), SPINAL-CORD, LIGHT-MICROSCOPY, WHITE-MATTER |
| Description: | 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 facilitate high spatial resolution and high SNR images, cutting‐edge diffusion contrasts, and direct comparison with histological data as a 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 concludes a three‐part series of recommendations and considerations for preclinical dMRI. Herein, we describe best practices for dMRI of ex vivo tissue, with a focus on image pre‐processing, data processing, and comparisons with microscopy. 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. We end by providing guidelines on code sharing and data sharing and point toward open‐source software and databases specific to small animal and ex vivo imaging. |
| Document Type: | Article Other literature type |
| File Description: | application/pdf |
| Language: | English |
| ISSN: | 1522-2594 0740-3194 |
| DOI: | 10.1002/mrm.30424 |
| DOI: | 10.48550/arxiv.2411.05021 |
| Access URL: | https://pubmed.ncbi.nlm.nih.gov/40008460 http://arxiv.org/abs/2411.05021 http://hdl.handle.net/11351/12974 https://dspace.library.uu.nl/handle/1874/460842 http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_AA99E2683A183 https://serval.unil.ch/notice/serval:BIB_AA99E2683A18 https://serval.unil.ch/resource/serval:BIB_AA99E2683A18.P001/REF.pdf https://hdl.handle.net/10067/2133390151162165141 https://repository.uantwerpen.be/docstore/d:irua:28142 https://pure.au.dk/portal/en/publications/303e2cdf-f5f6-4fd0-a953-d79f6520abd7 https://kclpure.kcl.ac.uk/portal/en/publications/d11e4490-9c34-4760-86f3-92df6316adfe http://www.scopus.com/inward/record.url?scp=85219588052&partnerID=8YFLogxK https://pure.au.dk/portal/en/publications/303e2cdf-f5f6-4fd0-a953-d79f6520abd7 https://doi.org/10.1002/mrm.30424 |
| Rights: | CC BY |
| Accession Number: | edsair.doi.dedup.....7813e9f10d61f779bc04176459d74250 |
| Database: | OpenAIRE |
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Nájsť tento článok vo Web of Science | 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 facilitate high spatial resolution and high SNR images, cutting‐edge diffusion contrasts, and direct comparison with histological data as a 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 concludes a three‐part series of recommendations and considerations for preclinical dMRI. Herein, we describe best practices for dMRI of ex vivo tissue, with a focus on image pre‐processing, data processing, and comparisons with microscopy. 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. We end by providing guidelines on code sharing and data sharing and point toward open‐source software and databases specific to small animal and ex vivo imaging. |
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| ISSN: | 15222594 07403194 |
| DOI: | 10.1002/mrm.30424 |