Solved problems for Granger causality in neuroscience: A response to Stokes and Purdon
Open accessAbstract
Granger-Geweke causality (GGC) is a powerful and popular method for identifying directed functional ('causal') connectivity in neuroscience. In a recent paper, Stokes and Purdon (2017b) raise several concerns about its use. They make two primary claims: (1) that GGC estimates may be severely biased or of high variance, and (2) that GGC fails to reveal the full structural/causal mechanisms of a system. However, these claims rest, respectively, on an incomplete evaluation of the literature, and a misconception about what GGC can be said to measure. Here we explain how existing approaches resolve the first issue, and discuss the frequently-misunderstood distinction between functional and effective neural connectivity which underlies Stokes and Purdon's second claim.
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Each is checked against this paper’s own text: does it say what the citing paper says it does?
These sample sizes were utilised on the basis of previous published research and pilot studies.
“These sample sizes were utilised on the basis of previous published research [11, 44, 45] and pilot studies.”
Cites
Ten simple rules for dynamic causal modeling
Stephan, K. E., Penny, W. D., Moran, R. J., den Ouden, H. E. M., Daunizeau, J., & Friston, K. J. (2010) · NeuroImage · doi:10.1016/j.neuroimage.2009.11.015 · Cited by 803 · see citing works
Thalamic amplification of cortical connectivity sustains attentional control
Schmitt, L. I., Wimmer, R. D., Nakajima, M., Happ, M., Mofakham, S., & Halassa, M. M. (2017) · Nature · doi:10.1038/nature22073 · Cited by 663 · see citing works
Bidirectional prefrontal-hippocampal interactions support context-guided memory
Place, R., Farovik, A., Brockmann, M., & Eichenbaum, H. (2016) · Nature Neuroscience · doi:10.1038/nn.4327 · Cited by 200 · cited 2× · see citing works
“This is important to note because our MVGC toolbox has been widely adopted within the community, with > 3;500 downloads and a significant number of high-impact research publications using the method (e.g., Yellin et al., 2015; Bruneau et al., 2015; Place et al., 2016; Schmitt et al., 2017; Wilber et al., 2017).”
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Haddon, J. E., Titherage, D., Heckenast, J. R., Carter, J., Owen, M. J., Hall, J., Wilkinson, L. S., & Jones, M. W. (2024) · Translational Psychiatry · doi:10.1038/s41398-024-02969-x · Cited by 6 · see citing works
“These sample sizes were utilised on the basis of previous published research [11, 44, 45] and pilot studies.”
Method
- Authors
- Barnett, L., Barrett, A. B., & Seth, A. K.
- Affiliations
- University of Sussex (GB)
- Corresponding author
- Seth, Anil K.
- Venue
- NeuroImage
- Publisher
- Elsevier BV
- Published
- 2018-09
- Volume
- 178
- Pages
- 744-748
- ISSN
- 1053-8119 (ISSN-L)
- OpenAlex
- W2805426804
- Cited by
- 73
- References
- 3
- Citations by year
- 2026: 4 · 2025: 1 · 2024: 10 · 2023: 9 · 2022: 13 · 2021: 18 · 2020: 7 · 2019: 6 · 2018: 5
- FWCI
- 5.36
- Type
- journal article
- Language
- en
- Open access
- green
- sro.sussex.ac.uk
- Licence
- Locations
- NeuroImage (publishedVersion)
- PubMed (publishedVersion)
- Sussex Research Online (University of Sussex) (submittedVersion, cc-by-nc-nd)
- Figshare (submittedVersion, cc-by-nc-nd)
- Funders
- Engineering and Physical Sciences Research Council (EP/L005131/1)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Life Sciences › Neuroscience › Cognitive Neuroscience › Neural dynamics and brain function
- Social Sciences › Psychology › Experimental and Cognitive Psychology › Mental Health Research Topics
- Keywords
- directed functional connectivity, effective connectivity, functional connectivity, estimation bias, estimation variance, causal mechanisms, neural network dynamics
- MeSH terms
- Neurosciences, Rest
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