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

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.

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

  • 8,099
    views
  • 718
    downloads
  • 120
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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)

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

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

  1. Jérôme Dockès
  2. Russell A Poldrack
  3. Romain Primet
  4. Hande Gözükan
  5. Tal Yarkoni
  6. Fabian Suchanek
  7. Bertrand Thirion
  8. Gael Varoquaux
(2020)
NeuroQuery, comprehensive meta-analysis of human brain mapping
eLife 9:e53385.
https://doi.org/10.7554/eLife.53385

Share this article

https://doi.org/10.7554/eLife.53385

Further reading

    1. Neuroscience
    Gyeong Hee Pyeon, Hyewon Cho ... Yong Sang Jo
    Research Article

    Recent studies suggest that calcitonin gene-related peptide (CGRP) neurons in the parabrachial nucleus (PBN) represent aversive information and signal a general alarm to the forebrain. If CGRP neurons serve as a true general alarm, their activation would modulate both passive nad active defensive behaviors depending on the magnitude and context of the threat. However, most prior research has focused on the role of CGRP neurons in passive freezing responses, with limited exploration of their involvement in active defensive behaviors. To address this, we examined the role of CGRP neurons in active defensive behavior using a predator-like robot programmed to chase mice. Our electrophysiological results revealed that CGRP neurons encode the intensity of aversive stimuli through variations in firing durations and amplitudes. Optogenetic activation of CGRP neuron during robot chasing elevated flight responses in both conditioning and retention tests, presumably by amyplifying the perception of the threat as more imminent and dangerous. In contrast, animals with inactivated CGRP neurons exhibited reduced flight responses, even when the robot was programmed to appear highly threatening during conditioning. These findings expand the understanding of CGRP neurons in the PBN as a critical alarm system, capable of dynamically regulating active defensive behaviors by amplifying threat perception, ensuring adaptive responses to varying levels of danger.

    1. Neuroscience
    Mi-Seon Kong, Ethan Ancell ... Larry S Zweifel
    Research Article

    The central amygdala (CeA) has emerged as an important brain region for regulating both negative (fear and anxiety) and positive (reward) affective behaviors. The CeA has been proposed to encode affective information in the form of valence (whether the stimulus is good or bad) or salience (how significant is the stimulus), but the extent to which these two types of stimulus representation occur in the CeA is not known. Here, we used single cell calcium imaging in mice during appetitive and aversive conditioning and found that majority of CeA neurons (~65%) encode the valence of the unconditioned stimulus (US) with a smaller subset of cells (~15%) encoding the salience of the US. Valence and salience encoding of the conditioned stimulus (CS) was also observed, albeit to a lesser extent. These findings show that the CeA is a site of convergence for encoding oppositely valenced US information.