A resting state fMRI analysis pipeline for pooling inference across diverse cohorts: an ENIGMA rs-fMRI protocol
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Large-scale consortium efforts such as Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) and other collaborative efforts show that combining statistical data from multiple independent studies can boost statistical power and achieve more accurate estimates of effect sizes, contributing to more reliable and reproducible research. A meta- analysis would pool effects from studies conducted in a similar manner, yet to date, no such harmonized protocol exists for resting state fMRI (rsfMRI) data. Here, we propose an initial pipeline for multi-site rsfMRI analysis to allow research groups around the world to analyze scans in a harmonized way, and to perform coordinated statistical tests. The challenge lies in the fact that resting state fMRI measurements collected by researchers over the last decade vary widely, with variable quality and differing spatial or temporal signal-to-noise ratio (tSNR). An effective harmonization must provide optimal measures for all quality data. Here we used rsfMRI data from twenty-two independent studies with approximately fifty corresponding T1-weighted and rsfMRI datasets each, to (A) review and aggregate the state of existing rsfMRI data, (B) demonstrate utility of principal component analysis (PCA)-based denoising and (C) develop a deformable ENIGMA EPI template based on the representative anatomy that incorporates spatial distortion patterns from various protocols and populations.
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A temporal signal‐to‐noise ratio of 50.4 is at least comparable with that in many published large‐scale studies.
“A temporal signal‐to‐noise ratio of 50.4 is at least comparable with that in many published large‐scale studies 70.”
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Hoogman, M., Muetzel, R., Guimaraes, J. P., Shumskaya, E., Mennes, M., Zwiers, M. P., Jahanshad, N., Sudre, G., Wolfers, T., Earl, E. A., et al. (2019) · American Journal of Psychiatry · doi:10.1176/appi.ajp.2019.18091033 · Cited by 467 · see citing works
Self-citationOsadchiy, V., Mayer, E. A., Bhatt, R., Labus, J. S., Gao, L., Kilpatrick, L. A., Liu, C., Tillisch, K., Naliboff, B., Chang, L., et al. (2019) · Obesity Science & Practice · doi:10.1002/osp4.362 · Cited by 44 · see citing works
Tanaka, M. (2024) · Advances in Clinical and Experimental Medicine · doi:10.17219/acem/197425 · Cited by 27 · see citing works
Chehadi, A. C., Pereira de Lima, E., Detregiachi, C. R. P., Santos de Argollo Haber, R., Catharin, V. M. C. S., Fornari Laurindo, L., Engracia Valenti, V., Machado Galhardi, C., Tanaka, M., & Maria Barbalho, S. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27010465 · Cited by 8 · see citing works
- Authors
- Adhikari, B. M., Jahanshad, N., Shukla, D., Turner, J., Grotegerd, D., Dannlowski, U., Kugel, H., Engelen, J., Dietsche, B., Krug, A., Kircher, T., Fieremans, E., Veraart, J., Novikov, D. S., Boedhoe, P. S. W., van der Werf, Y. D., van den Heuvel, O. A., Ipser, J., Uhlmann, A., Stein, D. J., Dickie, E., Voineskos, A. N., Malhotra, A. K., Pizzagalli, F., Calhoun, V. D., Waller, L., Veer, I. M., Walter, H., Buchanan, R. W., Glahn, D. C., Hong, L. E., Thompson, P. M., & Kochunov, P.
- Affiliations
- University of Maryland, Baltimore (US)
- University of Southern California (US)
- Georgia State University (US)
- University of Münster (DE)
- Philipps University of Marburg (DE)
- New York University (US)
- Amsterdam UMC Location Vrije Universiteit Amsterdam (NL)
- University of Cape Town (ZA)
- Centre for Addiction and Mental Health (CA)
- Zucker Hillside Hospital (US)
- Mind Research Network (US)
- Charité – Universitätsmedizin Berlin (DE)
- Yale University (US)
- Corresponding author
- Adhikari, Bhim M.
- ORCID
- Adhikari, Bhim M.
- Jahanshad, Neda
- Turner, Jessica
- Grotegerd, Dominik
- Dannlowski, Udo
- Kugel, Harald
- Krug, Axel
- Kircher, Tilo
- Fieremans, Els
- Veraart, Jelle
- Novikov, Dmitry S.
- Ipser, Jonathan
- Uhlmann, Anne
- Stein, Dan J.
- Dickie, Erin
- Voineskos, Aristotle N.
- Malhotra, Anil K.
- Pizzagalli, Fabrizio
- Calhoun, Vince D.
- Waller, Lea
- Buchanan, Robert W.
- Glahn, David C.
- Hong, L. Elliot
- Thompson, Paul M.
- Kochunov, Peter
- Venue
- Brain Imaging and Behavior
- Published
- 2018-09-06
- Volume
- 13
- Issue
- 5
- Pages
- 1453-1467
- ISSN
- 1931-7557 (ISSN-L)
- 1931-7565
- PMC
- PMC6401353
- OpenAlex
- W2891144030
- Cited by
- 53
- References
- 89
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 2 · 2023: 10 · 2022: 6 · 2021: 11 · 2020: 12 · 2019: 6 · 2018: 1
- FWCI
- 1.00
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Brain Imaging and Behavior (publishedVersion)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- NIH (U54EB020403, U01MH108148, 2R01EB015611, R01MH112180, R01DA027680, R01MH085646)
- German Research Foundation (FOR2107:KI 588/15-1, FOR2107: DA 1151/5-1, FOR2017:KO 4291/4-1 and KR 3822/5-1)
- Postdoctoral Fellow of the Research Foundation - Flanders (12S1615N)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Keywords
- resting-state fMRI, mystery, meta-analysis, spatial distortion correction, signal-to-noise ratio, T1-weighted imaging, neuroimaging genetics, data analysis pipeline
- MeSH terms
- Adult, Aged, Brain, Brain Mapping, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Artifacts, Young Adult, Signal-To-Noise Ratio, Functional Neuroimaging
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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