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A resting state fMRI analysis pipeline for pooling inference across diverse cohorts: an ENIGMA rs-fMRI protocol

  • Bhim M. AdhikariEmail author
  • Neda Jahanshad
  • Dinesh Shukla
  • Jessica Turner
  • Dominik Grotegerd
  • Udo Dannlowski
  • Harald Kugel
  • Jennifer Engelen
  • Bruno Dietsche
  • Axel Krug
  • Tilo Kircher
  • Els Fieremans
  • Jelle Veraart
  • Dmitry S. Novikov
  • Premika S. W. Boedhoe
  • Ysbrand D. van der Werf
  • Odile A. van den Heuvel
  • Jonathan Ipser
  • Anne Uhlmann
  • Dan J. Stein
  • Erin Dickie
  • Aristotle N. Voineskos
  • Anil K. Malhotra
  • Fabrizio Pizzagalli
  • Vince D. Calhoun
  • Lea Waller
  • Ilja M. Veer
  • Hernik Walter
  • Robert W. Buchanan
  • David C. Glahn
  • L. Elliot Hong
  • Paul M. Thompson
  • Peter Kochunov
Original Research

Abstract

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.

Keywords

ENIGMA EPI template Large multi-site studies Processing pipelines 

Notes

Funding

Support was received from NIH grants U54 EB020403, U01MH108148, 2R01EB015611, R01MH112180, R01DA027680, R01MH085646. MarbG and MuenG (FOR2107 study): Work was supported by the German Research Foundation (DFG), grant numbers FOR2107; KI 588/15–1 to TK, DA 1151/5–1 to UD, KO 4291/4–1 and KR 3822/5–1 to AK. JV is a Postdoctoral Fellow of the Research Foundation - Flanders (FWO; grant number 12S1615N).

Compliance with ethical standards

Conflict of interest

There is no conflict of interest for any of the authors.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

11682_2018_9941_MOESM1_ESM.docx (40 kb)
ESM 1 (DOCX 40 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Bhim M. Adhikari
    • 1
    Email author
  • Neda Jahanshad
    • 2
  • Dinesh Shukla
    • 1
  • Jessica Turner
    • 3
  • Dominik Grotegerd
    • 4
  • Udo Dannlowski
    • 4
  • Harald Kugel
    • 5
  • Jennifer Engelen
    • 6
  • Bruno Dietsche
    • 6
  • Axel Krug
    • 6
  • Tilo Kircher
    • 6
  • Els Fieremans
    • 7
  • Jelle Veraart
    • 7
  • Dmitry S. Novikov
    • 7
  • Premika S. W. Boedhoe
    • 8
  • Ysbrand D. van der Werf
    • 8
  • Odile A. van den Heuvel
    • 8
  • Jonathan Ipser
    • 9
  • Anne Uhlmann
    • 9
  • Dan J. Stein
    • 9
  • Erin Dickie
    • 10
  • Aristotle N. Voineskos
    • 11
    • 12
  • Anil K. Malhotra
    • 13
  • Fabrizio Pizzagalli
    • 2
  • Vince D. Calhoun
    • 14
  • Lea Waller
    • 15
  • Ilja M. Veer
    • 15
  • Hernik Walter
    • 15
  • Robert W. Buchanan
    • 1
  • David C. Glahn
    • 16
  • L. Elliot Hong
    • 1
  • Paul M. Thompson
    • 2
  • Peter Kochunov
    • 1
  1. 1.Maryland Psychiatric Research Center, Department of PsychiatryUniversity of Maryland School of MedicineBaltimoreUSA
  2. 2.Imaging Genetics Center, Keck School of Medicine of USCLos AngelesUSA
  3. 3.Department of PsychologyGeorgia State UniversityAtlantaUSA
  4. 4.Department of PsychiatryUniversity of MünsterMünsterGermany
  5. 5.Department of Clinical RadiologyUniversity of MünsterMünsterGermany
  6. 6.Department of Psychiatry and PsychotherapyPhilipps-University MarburgMarburgGermany
  7. 7.Center for Biomedical Imaging, Department of RadiologyNew York University School of MedicineNew YorkUSA
  8. 8.Department of Psychiatry, Department of Anatomy & NeurosciencesVU University Medical CenterAmsterdamNetherlands
  9. 9.Department of Psychiatry and Mental HealthUniversity of Cape TownCape TownSouth Africa
  10. 10.Centre for Addiction and Mental HealthTorontoCanada
  11. 11.Centre for Addiction and Mental HealthCampbell Family Mental Health Research InstituteTorontoCanada
  12. 12.Department of PsychiatryUniversity of TorontoTorontoCanada
  13. 13.Department of PsychiatryThe Zucker Hillside HospitalNew YorkUSA
  14. 14.The Mind Research Network & The University of New MexicoAlbuquerqueUSA
  15. 15.Department of Psychiatry and PsychotherapyCharité Universitätsmedizin BerlinBerlinGermany
  16. 16.Department of PsychiatryYale University, School of MedicineNew HavenUSA

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