how to easily organize and share neuroimaging data materials/reproducibility - 3...how to easily...
TRANSCRIPT
How to easily organize and
share neuroimaging dataChris GorgolewskiCenter for Reproducible Neuroscince
Stanford University
Neuroimaging data sharing hierarchy
Poldrack and Gorgolewski, 2014
Just coordinates?
• Databases such as Neurosynth or BrainMap rely on peak coordinates reported in papers (only strong effects)
Are we throwing money away?
NeuroVault.orgsimple data sharing
•Minimize the cost!
•We just want your statistical maps with minimum description (DOI)
• If you want you can put more metadata, but you don’t have to
•We streamline login process (Google, Facebook)
NeuroVault.org
Gorgolewski, et al., submitted
Benefits - visualisation
Benefits - decoding
Benefits - other
•Private collections
•Multiple contributors to one collection
•Sharable persistent URLs
•Viewer embeddable on your labs website or your private blog
• Improved exposure of your research
• Improved reusability of your results
Validation and gains in sensitivity
NeuroVault for developers
•RESTful API (field tested by Neurosynth)
•Source code available on GitHub
What is NIDM-Results?
MAKING DATASHARING countCredit where credit’s due
Quality control
•Share your stat maps!
Complex datasets require
elaborate descriptions
•Share your stat maps!
How can we appropriately
reward extra effort and risk
related with sharing data?
Solution – data papers
•Authors get recognizable credit for their work.
•Even smaller contributors such as RAs can be included.
•Acquisition methods are described in detail.
•Quality of metadata is being controlled by peer review.
Gorgolewski, Milham, and Margulies, 2013
Where to publish data papers?
•Neuroinformatics (Springer)
•GigaScience (BGI, BioMed Central)
•Scientific Data (Nature Publising Group)
•F1000Research (Faculty of 1000)
•Data in Brief (Elsevier)
•Journal of Open Psychology Data (Ubiquity press)
What makes a good data paper?
•Clear and accurate description of the acquisition protocol.
•Good data organization.
•Ease of access to data.
•Data quality description.
•Fair credit attribution.
How to improve the impact of your dataset?
•Provide preprocessed data.
•Reach out to your peers…
•…and people outside of your field (ML)
•Build a community around the data.
StudyForrest.org
Repositories
•Field specific
•OpenfMRI.org
•FCP/INDI (must include resting state fMRI)
•COINS
•Field agnostic
•DataVerse (Harvard)
•Figshare (only small datasets)
•DataDryad (fees may apply)
OpenfMRI
•Will host any dataset that has a task based fMRI component
•No fees
•Curated and uncurated datasets
•Recommended by many journals (including Scientific Data)
Prepare in advance
•Make sure your consent form includes data sharing
•Decide which database you want to send your data to in advance
•Organize your data according to their requirements
•Work on anonymized data as much as you can
Brain Imaging Data Structure
bids.neuroimaging.io
Ultimate consent form
• Inform participants about your intention to share data
•Explain the benefits
•Discuss the risks
open-brain-consent.readthedocs.org
Acknowledgements
Russell A. Poldrack
Jean-Baptiste Poline
Yannick Schwarz
Tal Yarkoni
Michael Milham
Daniel Margulies
Yannick Schwartz
Gael Varoquox
Joseph Wexler
Gabriel Rivera
Camile Maumet
Vanessa Sochat
Thomas Nichols
MPI CBS Resting state group
Poldrack Lab
INCF Data Sharing Task Force