How to easily organize and share neuroimaging data Materials/Reproducibility - 3...How to easily...

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