1. Neuroscience

Neuroscout, a unified platform for generalizable andreproducible fMRI research

  1. Alejandro de la Vega  Is a corresponding author
  2. Roberta Rocca
  3. Ross W Blair
  4. Christopher J Markiewicz
  5. Jeff Mentch
  6. James D Kent
  7. Peer Herholz
  8. Satrajit S Ghosh
  9. Russell A Poldrack
  10. Tal Yarkoni
  1. The University of Texas at Austin, United States
  2. Aarhus University, Denmark
  3. Stanford University, United States
  4. Massachusetts Institute of Technology, United States
  5. McGill University, Canada
https://doi.org/10.7554/eLife.79277
Share this article
Cite this article
  1. Alejandro de la Vega
  2. Roberta Rocca
  3. Ross W Blair
  4. Christopher J Markiewicz
  5. Jeff Mentch
  6. James D Kent
  7. Peer Herholz
  8. Satrajit S Ghosh
  9. Russell A Poldrack
  10. Tal Yarkoni
(2022)
Neuroscout, a unified platform for generalizable andreproducible fMRI research
eLife 11:e79277.
https://doi.org/10.7554/eLife.79277
  2. Download BibTeX
  3. Download .RIS

Abstract

Functional magnetic resonance imaging (fMRI) has revolutionized cognitive neuroscience, but methodological barriers limit the generalizability of findings from the lab to the real world. Here, we present Neuroscout, an end-to-end platform for analysis of naturalistic fMRI data designed to facilitate the adoption of robust and generalizable research practices. Neuroscout leverages state-of-the-art machine learning models to automatically annotate stimuli from dozens of fMRI studies using naturalistic stimuli-such as movies and narratives-allowing researchers to easily test neuroscientific hypotheses across multiple ecologically-valid datasets. In addition, Neuroscout builds on a robust ecosystem of open tools and standards to provide an easy-to-use analysis builder and a fully automated execution engine that reduce the burden of reproducible research. Through a series of meta-analytic case studies, we validate the automatic feature extraction approach and demonstrate its potential to support more robust fMRI research. Owing to its ease of use and a high degree of automation, Neuroscout makes it possible to overcome modeling challenges commonly arising in naturalistic analysis and to easily scale analyses within and across datasets, democratizing generalizable fMRI research.

Data availability

All code from our processing pipeline and core infrastructure is available online (https://www.github.com/neuroscout/neuroscout). An online supplement including all analysis code and resulting images is available as a public GitHub repository (https://github.com/neuroscout/neuroscout-paper).All analysis results are made publicly available in a public GitHub repository

The following previously published data sets were used
    1. Hanke M
    2. et al
    (2014) studyforrest
    OpenNeuro, doi:10.18112/ openneuro.ds000113 .v1.3.0.
    https://doi.org/10.18112/openneuro.ds000113.v1.3.0
    1. Nastase SA
    2. et al
    (2021) Narratives
    OpenNeuro, doi:10.18112/openneuro.ds002345 .v1.1.4.
    https://doi.org/10.18112/openneuro.ds002345.v1.1.4

Article and author information

Author details

  1. Alejandro de la Vega

    Department of Psychology, The University of Texas at Austin, Austin, United States
    For correspondence
    delavega@utexas.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9062-3778

  2. Roberta Rocca

    Interacting Minds Centre, Aarhus University, Aarhus, Denmark
    Competing interests
    The authors declare that no competing interests exist.

  3. Ross W Blair

    Department of Psychology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Christopher J Markiewicz

    Department of Psychology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6533-164X

  5. Jeff Mentch

    McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. James D Kent

    Department of Psychology, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Peer Herholz

    Montreal Neurological Institute, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9840-6257

  8. Satrajit S Ghosh

    McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5312-6729

  9. Russell A Poldrack

    Department of Psychology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Tal Yarkoni

    Department of Psychology, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Institute of Mental Health (R01MH109682)

  • Alejandro de la Vega
  • Roberta Rocca
  • Ross W Blair
  • Christopher J Markiewicz
  • Jeff Mentch
  • James D Kent
  • Peer Herholz
  • Satrajit S Ghosh
  • Russell A Poldrack
  • Tal Yarkoni

National Institute of Mental Health (R01MH096906)

  • Alejandro de la Vega
  • James D Kent
  • Tal Yarkoni

National Institute of Mental Health (R24MH117179)

  • Peer Herholz
  • Satrajit S Ghosh

National Institute of Mental Health (R24MH117179)

  • Ross W Blair
  • Christopher J Markiewicz
  • Russell A Poldrack

Canada First Research Excellence Fund

  • Peer Herholz

Brain Canada Fondation

  • Peer Herholz

Unifying Neuroscience and Artificial Intelligence - Québec

  • Peer Herholz

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

Copyright

© 2022, de la Vega 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

  • 1,365
    views
  • 236
    downloads
  • 6
    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. Alejandro de la Vega
  2. Roberta Rocca
  3. Ross W Blair
  4. Christopher J Markiewicz
  5. Jeff Mentch
  6. James D Kent
  7. Peer Herholz
  8. Satrajit S Ghosh
  9. Russell A Poldrack
  10. Tal Yarkoni
(2022)
Neuroscout, a unified platform for generalizable andreproducible fMRI research
eLife 11:e79277.
https://doi.org/10.7554/eLife.79277

Share this article

https://doi.org/10.7554/eLife.79277

Categories and tags

Research organism

Further reading

    1. Neuroscience

    The reuniens nucleus of the thalamus facilitates hippocampo-cortical dialogue during sleep

    Diellor Basha, Amirmohammad Azarmehri ... Igor Timofeev
    Research Article

    Memory consolidation during sleep depends on the interregional coupling of slow waves, spindles, and sharp wave-ripples (SWRs), across the cortex, thalamus, and hippocampus. The reuniens nucleus of the thalamus, linking the medial prefrontal cortex (mPFC) and the hippocampus, may facilitate interregional coupling during sleep. To test this hypothesis, we used intracellular, extracellular unit and local field potential recordings in anesthetized and head restrained non-anesthetized cats as well as computational modelling. Electrical stimulation of the reuniens evoked both antidromic and orthodromic intracellular mPFC responses, consistent with bidirectional functional connectivity between mPFC, reuniens and hippocampus in anesthetized state. The major finding obtained from behaving animals is that at least during NREM sleep hippocampo-reuniens-mPFC form a functional loop. SWRs facilitate the triggering of thalamic spindles, which later reach neocortex. In return, transition to mPFC UP states increase the probability of hippocampal SWRs and later modulate spindle amplitude. During REM sleep hippocampal theta activity provides periodic locking of reuniens neuronal firing and strong crosscorrelation at LFP level, but the values of reuniens-mPFC crosscorrelation was relatively low and theta power at mPFC was low. The neural mass model of this network demonstrates that the strength of bidirectional hippocampo-thalamic connections determines the coupling of oscillations, suggesting a mechanistic link between synaptic weights and the propensity for interregional synchrony. Our results demonstrate the presence of functional connectivity in hippocampo-thalamo-cortical network, but the efficacy of this connectivity is modulated by behavioral state.

    1. Neuroscience

    Movies reveal the fine-grained organization of infant visual cortex

    Cameron T Ellis, Tristan S Yates ... Nicholas Turk-Browne
    Research Article

    Studying infant minds with movies is a promising way to increase engagement relative to traditional tasks. However, the spatial specificity and functional significance of movie-evoked activity in infants remains unclear. Here, we investigated what movies can reveal about the organization of the infant visual system. We collected fMRI data from 15 awake infants and toddlers aged 5–23 months who attentively watched a movie. The activity evoked by the movie reflected the functional profile of visual areas. Namely, homotopic areas from the two hemispheres responded similarly to the movie, whereas distinct areas responded dissimilarly, especially across dorsal and ventral visual cortex. Moreover, visual maps that typically require time-intensive and complicated retinotopic mapping could be predicted, albeit imprecisely, from movie-evoked activity in both data-driven analyses (i.e. independent component analysis) at the individual level and by using functional alignment into a common low-dimensional embedding to generalize across participants. These results suggest that the infant visual system is already structured to process dynamic, naturalistic information and that fine-grained cortical organization can be discovered from movie data.

    1. Neuroscience

    Post-ejaculatory inhibition of female sexual drive via heterogeneous neuronal ensembles in the medial preoptic area

    Kentaro K Ishii, Koichi Hashikawa ... Garret D Stuber
    Research Article

    Male ejaculation acutely suppresses sexual motivation in male mice. In contrast, relatively little is known about how male ejaculation affects sexual motivation and sexual behavior in female mice. How the brain responds to the completion of mating is also unclear. Here, by using a self-paced mating assay, we first demonstrate that female mice show decreased sexual motivation acutely after experiencing male ejaculation. By using brain-wide analysis of activity-dependent labeling, we next pin-pointed the medial preoptic area as a brain region strongly activated during the post-ejaculatory period. Furthermore, using freely moving in vivo calcium imaging to compare the neural activity of inhibitory and excitatory neurons in the medial preoptic area, we revealed that a subset of the neurons in this region responds significantly and specifically to male ejaculation but not to female-to-male sniffing or to male mounting. While there were excitatory and inhibitory neurons that showed increased response to male ejaculation, the response magnitude as well as the proportion of neurons responding to the event was significantly larger in the inhibitory neuron population. Next, by unbiased classification of their responses, we also found a subpopulation of neurons that increase their activity late after the onset of male ejaculation. These neurons were all inhibitory indicating that male ejaculation induces a prolonged inhibitory activity in the medial preoptic area. Lastly, we found that chemogenetic activation of medial preoptic area neurons that were active during the post-ejaculatory period, but not during appetitive or consummatory periods, were sufficient to suppress female sexual motivation. Together, our data illuminate the importance of the medial preoptic area as a brain node which encodes a negative signal that sustains a low sexual motivation state after the female mice experience ejaculation.