IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-50826-8.html
   My bibliography  Save this article

A standardized image processing and data quality platform for rodent fMRI

Author

Listed:
  • Gabriel Desrosiers-Grégoire

    (Douglas Mental Health University Institute
    McGill University)

  • Gabriel A. Devenyi

    (Douglas Mental Health University Institute
    McGill University)

  • Joanes Grandjean

    (Radboud University Medical Center
    Radboud University Medical Center)

  • M. Mallar Chakravarty

    (Douglas Mental Health University Institute
    McGill University
    McGill University
    McGill University)

Abstract

Functional magnetic resonance imaging in rodents holds great potential for advancing our understanding of brain networks. Unlike the human community, there remains no standardized resource in rodents for image processing, analysis and quality control, posing significant reproducibility limitations. Our software platform, Rodent Automated Bold Improvement of EPI Sequences, is a pipeline designed to address these limitations for preprocessing, quality control, and confound correction, along with best practices for reproducibility and transparency. We demonstrate the robustness of the preprocessing workflow by validating performance across multiple acquisition sites and both mouse and rat data. Building upon a thorough investigation into data quality metrics across acquisition sites, we introduce guidelines for the quality control of network analysis and offer recommendations for addressing issues. Taken together, this software platform will allow the emerging community to adopt reproducible practices and foster progress in translational neuroscience.

Suggested Citation

  • Gabriel Desrosiers-Grégoire & Gabriel A. Devenyi & Joanes Grandjean & M. Mallar Chakravarty, 2024. "A standardized image processing and data quality platform for rodent fMRI," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50826-8
    DOI: 10.1038/s41467-024-50826-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-50826-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-50826-8?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Mathias, Adolf & Grond, Florian & Guardans, Ramon & Seese, Detlef & Canela, Miguel & Diebner, Hans H., 2004. "Algorithms for Spectral Analysis of Irregularly Sampled Time Series," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 11(i02).
    2. Joanes Grandjean & Alberto Corcoba & Martin C. Kahn & A. Louise Upton & Evan S. Deneris & Erich Seifritz & Fritjof Helmchen & Isabelle M. Mansuy & Edward O. Mann & Markus Rudin & Bechara J. Saab, 2019. "A brain-wide functional map of the serotonergic responses to acute stress and fluoxetine," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    3. Rotem Botvinik-Nezer & Felix Holzmeister & Colin F. Camerer & Anna Dreber & Juergen Huber & Magnus Johannesson & Michael Kirchler & Roni Iwanir & Jeanette A. Mumford & R. Alison Adcock & Paolo Avesani, 2020. "Variability in the analysis of a single neuroimaging dataset by many teams," Nature, Nature, vol. 582(7810), pages 84-88, June.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Christoph Huber & Christian König-Kersting & Matteo M. Marini, 2022. "Experimenting with Financial Professionals," Working Papers 2022-07, Faculty of Economics and Statistics, Universität Innsbruck, revised Jun 2024.
    2. Nick Huntington‐Klein & Andreu Arenas & Emily Beam & Marco Bertoni & Jeffrey R. Bloem & Pralhad Burli & Naibin Chen & Paul Grieco & Godwin Ekpe & Todd Pugatch & Martin Saavedra & Yaniv Stopnitzky, 2021. "The influence of hidden researcher decisions in applied microeconomics," Economic Inquiry, Western Economic Association International, vol. 59(3), pages 944-960, July.
    3. Dennis Bontempi & Leonard Nuernberg & Suraj Pai & Deepa Krishnaswamy & Vamsi Thiriveedhi & Ahmed Hosny & Raymond H. Mak & Keyvan Farahani & Ron Kikinis & Andrey Fedorov & Hugo J. W. L. Aerts, 2024. "End-to-end reproducible AI pipelines in radiology using the cloud," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    4. Matthew Rosenblatt & Link Tejavibulya & Rongtao Jiang & Stephanie Noble & Dustin Scheinost, 2024. "Data leakage inflates prediction performance in connectome-based machine learning models," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Jessica Dafflon & Pedro F. Da Costa & František Váša & Ricardo Pio Monti & Danilo Bzdok & Peter J. Hellyer & Federico Turkheimer & Jonathan Smallwood & Emily Jones & Robert Leech, 2022. "A guided multiverse study of neuroimaging analyses," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    6. Dreber, Anna & Johannesson, Magnus, 2023. "A framework for evaluating reproducibility and replicability in economics," Ruhr Economic Papers 1055, RWI - Leibniz-Institut für Wirtschaftsforschung, Ruhr-University Bochum, TU Dortmund University, University of Duisburg-Essen.
    7. Christophe Pérignon & Olivier Akmansoy & Christophe Hurlin & Anna Dreber & Felix Holzmeister & Juergen Huber & Magnus Johanneson & Michael Kirchler & Albert Menkveld & Michael Razen & Utz Weitzel, 2022. "Reproducibility of Empirical Results: Evidence from 1,000 Tests in Finance," Working Papers hal-03810013, HAL.
    8. Joakim A. Weill & Matthieu Stigler & Olivier Deschenes & Michael R. Springborn, 2021. "Researchers' Degrees-of-Flexibility and the Credibility of Difference-in-Differences Estimates: Evidence From the Pandemic Policy Evaluations," NBER Working Papers 29550, National Bureau of Economic Research, Inc.
    9. Nate Breznau & Eike Mark Rinke & Alexander Wuttke & Hung H. V. Nguyen & Muna Adem & Jule Adriaans & Amalia Alvarez-Benjumea & Henrik K. Andersen & Daniel Auer & Flavio Azevedo & Oke Bahnsen & Dave Bal, 2022. "Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty," Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, vol. 119(44), pages 2203150119-, November.
    10. Feng Zhou & Weihua Zhao & Ziyu Qi & Yayuan Geng & Shuxia Yao & Keith M. Kendrick & Tor D. Wager & Benjamin Becker, 2021. "A distributed fMRI-based signature for the subjective experience of fear," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    11. Dario Krpan & Jonathan E. Booth & Andreea Damien, 2023. "The positive–negative–competence (PNC) model of psychological responses to representations of robots," Nature Human Behaviour, Nature, vol. 7(11), pages 1933-1954, November.
    12. Andrea I. Luppi & Helena M. Gellersen & Zhen-Qi Liu & Alexander R. D. Peattie & Anne E. Manktelow & Ram Adapa & Adrian M. Owen & Lorina Naci & David K. Menon & Stavros I. Dimitriadis & Emmanuel A. Sta, 2024. "Systematic evaluation of fMRI data-processing pipelines for consistent functional connectomics," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    13. Gabriel Nova & Sander van Cranenburgh & Stephane Hess, 2024. "Understanding the decision-making process of choice modellers," Papers 2411.01704, arXiv.org.
    14. Nate Breznau & Eike Mark Rinke & Alexander Wuttke & Hung H. V. Nguyen & Muna Adem & Jule Adriaans & Amalia Alvarez-Benjumea & Henrik K. Andersen & Daniel Auer & Flavio Azevedo & Oke Bahnsen & Dave Bal, 2022. "Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty," Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, vol. 119(44), pages 2203150119-, November.
    15. Schweinsberg, Martin & Feldman, Michael & Staub, Nicola & van den Akker, Olmo R. & van Aert, Robbie C.M. & van Assen, Marcel A.L.M. & Liu, Yang & Althoff, Tim & Heer, Jeffrey & Kale, Alex & Mohamed, Z, 2021. "Same data, different conclusions: Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis," Organizational Behavior and Human Decision Processes, Elsevier, vol. 165(C), pages 228-249.
    16. Christoph Huber & Anna Dreber & Jürgen Huber & Magnus Johannesson & Michael Kirchler & Utz Weitzel & Miguel Abellán & Xeniya Adayeva & Fehime Ceren Ay & Kai Barron & Zachariah Berry & Werner Bönte , 2023. "Competition and moral behavior: A meta-analysis of forty-five crowd-sourced experimental designs," Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, vol. 120(23), pages 2215572120-, June.
    17. Felix Holzmeister & Magnus Johannesson & Robert Böhm & Anna Dreber & Jürgen Huber & Michael Kirchler, 2023. "Heterogeneity in effect size estimates: Empirical evidence and practical implications," Working Papers 2023-17, Faculty of Economics and Statistics, Universität Innsbruck.
    18. Campbell, Douglas & Brodeur, Abel & Dreber, Anna & Johannesson, Magnus & Kopecky, Joseph & Lusher, Lester & Tsoy, Nikita, 2024. "The Robustness Reproducibility of the American Economic Review," I4R Discussion Paper Series 124, The Institute for Replication (I4R).
    19. Chin, Jason & Zeiler, Kathryn, 2021. "Replicability in Empirical Legal Research," LawArXiv 2b5k4, Center for Open Science.
    20. Sadri, Arash, 2022. "The Ultimate Cause of the “Reproducibility Crisis”: Reductionist Statistics," MetaArXiv yxba5, Center for Open Science.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50826-8. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.