My research centres on making neuroimaging more rigorous and reproducible. This spans three overlapping areas: community standards for data organisation and sharing, statistical methods for M/EEG and fMRI, and the tools and infrastructure that make open science tractable at scale.

Research Themes

Open Neuroimaging Standards

Much of the field’s reproducibility problem is upstream of analysis — in how data are collected, described, and shared. I co-lead or contribute to several community efforts that define how this should work: BIDS extensions for EEG, Genetics, and PET; the OHBM COBIDAS guidelines for M/EEG and MRI; and the Open Brain Consent templates that allow participants to authorise open sharing under GDPR. The common thread is building community consensus around practices that make individual studies reusable.

Related: COBIDAS MEEG · BIDS · Open Brain Consent

Statistical Methods for Neuroimaging

Standard parametric methods applied mass-univariately at the sensor or voxel level carry assumptions that are routinely violated in neuroimaging data — non-normality, outliers, mis-specified models, and inflated false positives from multiple comparisons. I develop and maintain tools for robust estimation (trimmed means, robust correlations, Winsorised statistics), hierarchical GLM for EEG/MEG (LIMO MEEG), adaptive thresholding for single-subject fMRI maps, and methods for single-trial ERP analysis.

Related: LIMO MEEG · SPMup · Robust Statistical Toolbox

Brain Structure, Function & Cognition

Empirically, my work spans face and object processing (ERP latencies and magnitudes), fMRI task design and signal quality, vascular parcellation of the cortex, and — more recently — transdiagnostic psychopathology and pain–reward interactions. A consistent methodological concern is whether the numbers we report are well-defined and interpretable: % signal change, effect sizes, confidence intervals, and visualisations that convey uncertainty honestly.


Selected Publications

Reproducibility & Best Practices

  • Issues and recommendations from the OHBM COBIDAS MEEG committee for reproducible EEG and MEG research Pernet, C., Garrido, M., Gramfort, A., Maurits, N., Michel, C., Pang, E., Salmelin, R., Schoffelen, JM., Valdes-Sosa, P., & Puce, A. (2020) Nature Neuroscience
  • Open and reproducible neuroimaging: from study inception to publication Niso, G. et al. (2022) NeuroImage, 119623
  • Improving functional magnetic resonance imaging reproducibility Pernet, C. & Poline, J-B. (2015) GigaScience, 4, 15
  • Data visualization for inference in tomographic brain imaging Pernet, C. R. & Madan, C. R. (2019) European Journal of Neuroscience, 51, 695–705
  • Improving standards in brain-behavior correlation analyses Rousselet, G. A. & Pernet, C. R. (2012) Frontiers in Human Neuroscience, 6, 119
  • Can We Standardize Clinical Functional Neuroimaging Procedures? Beisteiner, R., Pernet, C. R. & Stippich, C. (2019) Frontiers in Neurology, 8, 1153
  • Brainhack: developing a culture of open, inclusive, community-driven neuroscience Gau, R. et al. (2021) Neuron, 109, 1769–1775
  • Visual object categorization in the brain: what can we really learn from ERP peaks? Rousselet, G. A., Pernet, C. R., Caldara, R. & Schyns, P. G. (2011) Frontiers in Human Neuroscience, 5, 156
  • Quantifying the Time Course of Visual Object Processing Using ERPs: It's Time to Up the Game Rousselet, G. A. & Pernet, C. R. (2011) Frontiers in Psychology, 2, 107
  • Single-trial analyses: why bother? Pernet, C. R., Sajda, P. & Rousselet, G. A. (2011) Frontiers in Psychology, 2, 322

Open Data & Standards

  • EEG-BIDS, an extension to the brain imaging data structure for electroencephalography Pernet, C. R., Appelhoff, S., Gorgolewski, K., Flandin, G., Phillips, C., Delorme, A. & Oostenveld, R. (2019) Scientific Data, 6, 103
  • PET-BIDS, an extension to the brain imaging data structure for positron emission tomography Nørgaard, M. et al. (2022) Scientific Data, 9, 65
  • The genetics-BIDS extension: Easing the search for genetic data associated with human brain imaging Moreau, C., Jean-Louis, M., Ross, B., Markiewicz, C., Turner, J., Calhoun, V., Nichols, T. & Pernet, C. (2020) GigaScience, 9(10), giaa104
  • The Open Brain Consent: Informing research participants and obtaining consent to share brain imaging data The Open Brain Consent Working Group (2021) Human Brain Mapping
  • On the Long-term Archiving of Research Data Pernet, C., Svarer, C., Blair, R. et al. (2023) Neuroinformatics, 21, 243–246
  • Improving data availability for brain image biobanking in healthy subjects: practice-based suggestions from an international multidisciplinary working group Shenkin, S. D., Pernet, C., Nichols, T. E., Poline, J. B. et al. (2017) NeuroImage, 153, 399–409
  • Longitudinal multi-centre brain imaging studies: guidelines and practical tips for accurate and reproducible imaging endpoints and data sharing Wiseman, S. J., Meijboom, R., Valdés Hernández, M. D. C., Pernet, C. et al. (2019) Trials, 20, 1
  • #EEGManyLabs: Investigating the Replicability of Influential EEG Experiments Pavlov, Y. et al. (2021) Cerebral Cortex

Methods & Applications

  • Mixture model for single-subject fMRI thresholding Gorgolewski, K. et al. (2012) Frontiers in Human Neuroscience
  • BOLD signal decomposition: correcting HRF parameter estimates and computing percentage signal change Pernet, C. R. (2014) Frontiers in Neuroscience

Preprints


Full publication list on Google Scholar →