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Front Neuroinform. 2020 Jan 22;13:78. doi: 10.3389/fninf.2019.00078. eCollection 2019.

Animal Functional Magnetic Resonance Imaging: Trends and Path Toward Standardization.

Author information

Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore, Singapore.
Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.
Center for Animal MRI, Department of Neurology, Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
Direction de la Recherche Fondamentale, MIRCen, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Fontenay-aux-Roses, France.
Neurodegenerative Diseases Laboratory, Centre National de la Recherche Scientifique, UMR 9199, Université Paris-Sud, Université Paris-Saclay, Fontenay-aux-Roses, France.
Biomedical MR Imaging and Spectroscopy Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.
Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada.
Department of Biological and Biomedical Engineering, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada.
Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Centre for Neuroscience and Cognitive Systems @ UNITN, Rovereto, Italy.
Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
Department of Biomedical Engineering, Georgia Tech, Emory University, Atlanta, GA, United States.
Hospital for Sick Children, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
Wellcome Centre for Integrative NeuroImaging, University of Oxford, Oxford, United Kingdom.
Department of Radiology and Nuclear Medicine, Donders Institute for Brain, Cognition, and Behaviour, Donders Institute, Radboud University Medical Center, Nijmegen, Netherlands.


Animal whole-brain functional magnetic resonance imaging (fMRI) provides a non-invasive window into brain activity. A collection of associated methods aims to replicate observations made in humans and to identify the mechanisms underlying the distributed neuronal activity in the healthy and disordered brain. Animal fMRI studies have developed rapidly over the past years, fueled by the development of resting-state fMRI connectivity and genetically encoded neuromodulatory tools. Yet, comparisons between sites remain hampered by lack of standardization. Recently, we highlighted that mouse resting-state functional connectivity converges across centers, although large discrepancies in sensitivity and specificity remained. Here, we explore past and present trends within the animal fMRI community and highlight critical aspects in study design, data acquisition, and post-processing operations, that may affect the results and influence the comparability between studies. We also suggest practices aimed to promote the adoption of standards within the community and improve between-lab reproducibility. The implementation of standardized animal neuroimaging protocols will facilitate animal population imaging efforts as well as meta-analysis and replication studies, the gold standards in evidence-based science.


DREADD; non-human primate; optogenetics; resting-state; rodent

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