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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
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    References listed on IDEAS

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    1. 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.
    2. 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).
    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.
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