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
Publishing your data
Outline
- Open science
- Towards open fMRI data
- Towards reproducible research
- A generic model for open neuroimaging research?
Research outcome
Research outcome
20200213_RMN_Open_fMRI_data
By Sylvain Takerkart
