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| Format: | Preprint |
| Published: |
2022
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2209.13371 |
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| _version_ | 1866913561903628288 |
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| author | Schilling, Kurt G Grussu, Francesco Ianus, Andrada Hansen, Brian Howard, Amy FD 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 Frydman, Lucio van de Looij, Yohan Hike, David Dunn, Jeff F Miller, Karla Landman, Bennett A Shemesh, Noam Anderson, Adam McKinnon, Emilie Farquharson, Shawna Acqua, Flavio Dell' 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 Bihan, Denis Le Blackband, Stephen J Ciobanu, Luisa Fieremans, Els Bai, Ruiliang Leergaard, Trygve Zhang, Jiangyang Dyrby, Tim B Johnson, G Allan Cohen-Adad, Julien Budde, Matthew D Jelescu, Ileana O |
| author_facet | Schilling, Kurt G Grussu, Francesco Ianus, Andrada Hansen, Brian Howard, Amy FD 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 Frydman, Lucio van de Looij, Yohan Hike, David Dunn, Jeff F Miller, Karla Landman, Bennett A Shemesh, Noam Anderson, Adam McKinnon, Emilie Farquharson, Shawna Acqua, Flavio Dell' 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 Bihan, Denis Le Blackband, Stephen J Ciobanu, Luisa Fieremans, Els Bai, Ruiliang Leergaard, Trygve Zhang, Jiangyang Dyrby, Tim B Johnson, G Allan Cohen-Adad, Julien Budde, Matthew D Jelescu, Ileana O |
| contents | The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher signal-to-noise ratio and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts. Another major advantage of ex vivo dMRI is the 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 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 3-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 give general considerations and foundational knowledge that must be considered when designing experiments. We 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2209_13371 |
| institution | arXiv |
| publishDate | 2022 |
| record_format | arxiv |
| spellingShingle | Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 -- Ex vivo imaging: added value and acquisition Schilling, Kurt G Grussu, Francesco Ianus, Andrada Hansen, Brian Howard, Amy FD 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 Frydman, Lucio van de Looij, Yohan Hike, David Dunn, Jeff F Miller, Karla Landman, Bennett A Shemesh, Noam Anderson, Adam McKinnon, Emilie Farquharson, Shawna Acqua, Flavio Dell' 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 Bihan, Denis Le Blackband, Stephen J Ciobanu, Luisa Fieremans, Els Bai, Ruiliang Leergaard, Trygve Zhang, Jiangyang Dyrby, Tim B Johnson, G Allan Cohen-Adad, Julien Budde, Matthew D Jelescu, Ileana O Medical Physics Tissues and Organs The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher signal-to-noise ratio and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts. Another major advantage of ex vivo dMRI is the 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 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 3-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 give general considerations and foundational knowledge that must be considered when designing experiments. We 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. |
| title | Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 -- Ex vivo imaging: added value and acquisition |
| topic | Medical Physics Tissues and Organs |
| url | https://arxiv.org/abs/2209.13371 |