Walking through the jungle towards open fMRI data and reproducible research

Sylvain Takerkart

http://int.univ-amu.fr

http://meca-brain.org

http://neuralbasesofcommunication.eu

w/ Virginia Aglieri, Bastien Cagna, Pascal Belin

Outline

  • Open science
  • Towards open fMRI data
  • Towards reproducible research
  • A generic model for open neuroimaging research?

Plan national pour la science ouverte (2018)

  • Deuxième axe : Structurer et ouvrir les données de la recherche
  • towards FAIR data (Facile à trouver, Accessible, Interoperable, Réutilisable)

  • "Rendre obligatoire la diffusion ouverte des données de recherche issues de programmes financés par appels à projets sur fonds publics."

  • "une politique de données ouvertes associées aux articles et le développement des data papers."

ANR LIVES 2015-2019

  • LIVES = Learning with Interacting ViEwS
  • partners 1-3 = developing machine learning algorithms
  • partners 4-5 = acquiring / designing multimodal data
  • our role in the project: produce data and make it accessible to the other partners (to test their algorithms)
  • we also promised to make it open...

Outline

  • Open science
  • Towards open fMRI data
  • Towards reproducible research
  • A generic model for open neuroimaging research?

A few tips...

  • uploading 230GB is a lot!
  • Open Neuro command line interface (CLI)
  • do not forget to deface (anonymisation)
  • pydeface

Online data analysis

  • fmriprep directly available on OpenNeuro (its outcome becomes part of the dataset)
  • direct link with BrainLife

Publishing your data

Outline

  • Open science
  • Towards open fMRI data
  • Towards reproducible research
  • A generic model for open neuroimaging research?

FAIR

  • data
  • metadata
  • source code

Findable, Accessible, Interpretable, Reusable

Reproducible research

Research to reproduce...

Storing preprocessed data

statistical maps: Neurovault

Generic data repository

Zenodo

Source code

https://github.com/SylvainTakerkart/inter_subject_pattern_analysis

Publishing your data

Outline

  • Open science
  • Towards open fMRI data
  • Towards reproducible research
  • A generic model for open neuroimaging research?

Research outcome

Research outcome

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