1. Neuroscience
Download icon

NeuroQuery, comprehensive meta-analysis of human brain mapping

  1. Jérôme Dockès  Is a corresponding author
  2. Russell A Poldrack
  3. Romain Primet
  4. Hande Gözükan
  5. Tal Yarkoni
  6. Fabian Suchanek
  7. Bertrand Thirion
  8. Gael Varoquaux  Is a corresponding author
  1. INRIA, France
  2. Stanford University, United States
  3. University of Texas at Austin, United States
  4. Télécom Paris University, France
Tools and Resources
  • Cited 9
  • Views 2,710
  • Annotations
Cite this article as: eLife 2020;9:e53385 doi: 10.7554/eLife.53385

Abstract

Reaching a global view of brain organization requires assembling evidence on widely different mental processes and mechanisms. The variety of human neuroscience concepts and terminology poses a fundamental challenge to relating brain imaging results across the scientific literature. Existing meta-analysis methods perform statistical tests on sets of publications associated with a particular concept. Thus, large-scale meta-analyses only tackle single terms that occur frequently. We propose a new paradigm, focusing on prediction rather than inference. Our multivariate model predicts the spatial distribution of neurological observations, given text describing an experiment, cognitive process, or disease. This approach handles text of arbitrary length and terms that are too rare for standard meta-analysis. We capture the relationships and neural correlates of 7547 neuroscience terms across 13459 neuroimaging publications. The resulting meta-analytic tool, neuroquery.org, can ground hypothesis generation and data-analysis priors on a comprehensive view of published findings on the brain.

Data availability

All the data that we can share without violating copyright (including word counts of publications) have been shared on https://github.com/neuroquery/ alongside with the analysis scripts. Everything is readily downloadable without any authorization or login required.

Article and author information

Author details

  1. Jérôme Dockès

    Parietal, INRIA, Palaiseau, France
    For correspondence
    jerome@dockes.org
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5304-2496
  2. Russell A Poldrack

    Department of Psychology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6755-0259
  3. Romain Primet

    Parietal, INRIA, Palaiseau, France
    Competing interests
    No competing interests declared.
  4. Hande Gözükan

    Parietal, INRIA, Palaiseau, France
    Competing interests
    No competing interests declared.
  5. Tal Yarkoni

    Department of Psychology, University of Texas at Austin, Austin, United States
    Competing interests
    No competing interests declared.
  6. Fabian Suchanek

    Data, Intelligence, and Graphs, Télécom Paris University, Palaiseau, France
    Competing interests
    No competing interests declared.
  7. Bertrand Thirion

    Parietal, INRIA, Paris, France
    Competing interests
    No competing interests declared.
  8. Gael Varoquaux

    Parietal, INRIA, Palaiseau, France
    For correspondence
    gael.varoquaux@inria.fr
    Competing interests
    Gael Varoquaux, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1076-5122

Funding

Digiteo (2016-1270D - Projet MetaCog)

  • Jérôme Dockès

National Institutes of Health (R01MH096906)

  • Tal Yarkoni

Agence Nationale de la Recherche (ANR-16- CE23-0007-01)

  • Fabian Suchanek

H2020 European Research Council (785907 (HBP SGA2))

  • Bertrand Thirion

H2020 European Research Council (826421 (VirtualbrainCloud))

  • Bertrand Thirion

Canada First Research Excellence Fund (Healthy Brains for Healthy Lives initiative)

  • Gael Varoquaux

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Thomas Yeo, National University of Singapore, Singapore

Publication history

  1. Received: November 6, 2019
  2. Accepted: March 3, 2020
  3. Accepted Manuscript published: March 4, 2020 (version 1)
  4. Version of Record published: April 17, 2020 (version 2)

Copyright

© 2020, Dockès et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,710
    Page views
  • 303
    Downloads
  • 9
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Neuroscience
    Jenna Nagy et al.
    Research Article Updated

    Output signals of neural circuits, including the retina, are shaped by a combination of excitatory and inhibitory signals. Inhibitory signals can act presynaptically on axon terminals to control neurotransmitter release and regulate circuit function. However, it has been difficult to study the role of presynaptic inhibition in most neural circuits due to lack of cell type-specific and receptor type-specific perturbations. In this study, we used a transgenic approach to selectively eliminate GABAA inhibitory receptors from select types of second-order neurons – bipolar cells – in mouse retina and examined how this affects the light response properties of the well-characterized ON alpha ganglion cell retinal circuit. Selective loss of GABAA receptor-mediated presynaptic inhibition causes an enhanced sensitivity and slower kinetics of light-evoked responses from ON alpha ganglion cells thus highlighting the role of presynaptic inhibition in gain control and temporal filtering of sensory signals in a key neural circuit in the mammalian retina.

    1. Medicine
    2. Neuroscience
    George A Mashour et al.
    Research Article

    Understanding how the brain recovers from unconsciousness can inform neurobiological theories of consciousness and guide clinical investigation. To address this question, we conducted a multicenter study of 60 healthy humans, half of whom received general anesthesia for three hours and half of whom served as awake controls. We administered a battery of neurocognitive tests and recorded electroencephalography to assess cortical dynamics. We hypothesized that recovery of consciousness and cognition is an extended process, with differential recovery of cognitive functions that would commence with return of responsiveness and end with return of executive function, mediated by prefrontal cortex. We found that, just prior to the recovery of consciousness, frontal-parietal dynamics returned to baseline. Consistent with our hypothesis, cognitive reconstitution after anesthesia evolved over time. Contrary to our hypothesis, executive function returned first. Early engagement of prefrontal cortex in recovery of consciousness and cognition is consistent with global neuronal workspace theory.