What’s involved?

Longitudinal Acquisition, Storage and Curation, Interoperability, Reproducibility, Transfer, Anonymization, Security, Privacy, Ethics, APIs, Validation, Quality Control, Protocol Checking, Preprocessing, Analysis, HPC, Provenance, Ontological Standarization,
Data Harmonization, Upgrades, Maintenance, Bug Fixes, User Interface, Javascript, Bootstrap, Tracking, Extensibility, Data Management, Summary Statistics, Workflows,
Development, Tool Integration, Data Sharing, Download, Multi-Modal Linking, Querying, Image Processing, Visualization, Networking, System Administration, Partnerships, Funding, HR ...No big deal!

LORIS-CBRAIN INTEGRATION

What is Data Sharing?

Exchange of information

Datasets

Tools

Standarization

Databases

Collaborations

Conferences, hackathons

Facebook, Google, Twitter, etc.


Image source: http://blog.veritythink.com/post/87880448269/creative-data-sharing-and-open-humanitarianism

Data Sharing Issues

Benefits Hurdles
It's the future Fear
Reduces waste/duplication Technical challenges
Increased exposure Privacy concerns
Access to larger datasets Data Harmonization
Access to rare data Interoperability
Less attrition Reproducibility
Increased validation Obtaining ethics
Saving Tax $$ Public dataset not identical

Privacy Concerns

Adrian Thorogood BIC lecture - March 9, 2016

Best practices in Data Sharing

Committee on Best Practices in Data Analysis and Sharing (COBIDAS)

COBIDAS - Key points

  1. Experimental Design
  2. Acquisition Reporting
  3. Preprocessing Reporting
  4. Statistical Modeling and Inference
  5. Results Reporting
  6. Data sharing
  7. Reproducibility

Centralized or Distributed?

Some Data Sharing solutions?

Global Data Sharing Initiatives

Public Data Repositories

CBRAIN hooks

BIDS

NIDM

Neurovault

Braincode interoperability

Interoperability with other competitors

Best practices

External Initiatives

INCF, Open Science Framework, NITRC, Allen Institute, NDAR, Open fMRI, Organization Human Brain Mapping, Human Brain Project, Compute Canada, Maelstrom, UK Biobank, Edinburgh BRAINS ImageBank, BRAIN, ENIGMA, Enhanced Nathan Kline Institute (1000 Functional Connectomes), LONI, GAAIN, COINS, XNAT, BrainSpell, VIP, SPM, BrainCode, FSL, FBIRN, Synapse, CIMA-Q, NeuroDevNet, GUSTO, QPN, The NeuroBureau, ABCD...

So many initiatives!

INCF - Los Angeles 2016

BIDS

Common Ontology for Imaging Data

NeuroImaging Data Model

Format for storing metadata, provenance, processing information

DataLad

Atlas template building

Goal:

To create standardized JSON metadata to describe atlases

For either volumetric or surface atlases

Pipelines (e.g.CIVET) can access more atlases for anatomical standardization

Consolidated datasets

ADNI, ICBM, NIHPD, Allen Mouse Brain, IBIS, Generation-R, ABIDE, ABIDE Preprocessed, ADHD 200, ADHD Preprocessed, Human Connectome Project, OMEGA, UK Biobank, Edinburgh Biobank, BigBrain, Talairach, 1000 Functional Connectomes, Colin 27, MNI 305, 1000 Brains, AAL, ANIMAL, MAVAN, PreventAD, PING, MNI 152, MNI 305, FSL...

So many datasets!

ADNI

  • Cited 343 times

  • Data-use agreements

  • Used for countless analyses

  • Restrictive
  • Cited 295 times
  • Control data for NDAR
  • Longitudinal study (8 years)
  • 532 subjects
  • 8000 distinct variables
  • 37000 individual assessments
  • T1, T2, PD, DTI, Spectroscopy
  • ∼3TB of imaging data
  • 2000 MRI acquisitions

ABIDE

BigBrain

Quebec Parkinson Network

Tools and Environments

Neurovault, NeuroSynth, CIVET, VIP, Boutiques, Git-Annex, SOLID, BIDS, NiDM, DiCAT, DCMTK, NiPype, ITK, Freesurfer, SPM, FSL, Mobile MRI, 1000 Brains, AAL, BrainCode, GitHub, Amazon Cloud, FSL, IDA, BrainVisa, DICOM Confidential, DockerHub, Gate, CMIND...

So many Tools!

Neurovault Example

BrainBrowser

Hackathons

Important value of hackathons to data sharing initiatives

LORIS - CBRAIN Data Flow

LORIS - Key features

LORIS Dashboard

LORIS globally

  • Cited 295 times
  • Control data for NDAR
  • Longitudinal study (8 years)
  • 532 subjects
  • 8000 distinct variables
  • 37000 individual assessments
  • T1, T2, PD, DTI, Spectroscopy
  • ∼3TB of imaging data
  • 2000 MRI acquisitions

  • Autism infant brain development
  • 3000+ scans
  • 700+ subjects
  • 7000 distinct variables
  • 150,000+ individual assessments
  • T1, T2, DTI, BOLD
  • ∼5 TBs imaging data
  • Genetic/biospecimen data

CCNA

  • $35 million

  • CIHR funded

  • Pan Canadian Consortium

  • Acquisition in June, 2016

  • 35 collections sites

  • LORIS powered

BigBrain

OMEGA

  • Open MEG Archive

  • First open MEG repository

  • 180 user accounts created

  • Associated structural data

  • 500+ reads on academia.edu

CBRAIN

Several default tools:

  • CIVET
  • CivetCombiner
  • CivetQC
  • Freesurfer
  • SPM-batch
  • NIAK
  • FSL (bedpostx, bet, fast, feat, first flirt, melodic, probtrackx)
  • Numerous converters
  • And many more...

cbrain-support.mni@mcgill.ca

CBRAIN projects

CBRAIN tasks

CIVET for neonates

Open Science

Cyberinfrastructure

Cybersecurity

What's in it for me?

More citations (Piwowar & Vision, 2013)

Access to larger datasets

Greater exposure

Validation of your data

More collaborations

Increased funding

LORIS Biobank instance

LORIS Imaging instance

Open Science Functionality

Acquisition & Storage Dissemination & Analysis
Organized/Accessible data Centralized repository
Long term storage Provenance Capture
Quality Control mechanisms API for interoperability
Web visualization Consent is factored in
Tablet/Mobile Friendly User account access control
Anonymized automatically Completely de-identified
Cross-modal linking Cross-study correlation
Online Data Querying Access to high performance computing

Thank you!Acknowledgements: Alan Evans, Alex Zijdenbos, Dario Vins, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastian Muehlboeck, Reza Adalat, Louis Collins, Vladimir Fonov, Marc Rousseau, Mia Petkova, Rathi Gnanasekaran, David Brownlee, Tarek Sherif, Pierre Rioux, Nic Kassis, Leigh MacIntyre, Claude Lepage, Ilana Leppert, Natasha Beck, Tristan Glatard, Bert Vincent, Lindsay Lewis, Najma Mahani, Elodie Portales-Casamar, Alden Woodward, Sylvain Milot, Jean Francois Malouin, Sylvain Baillet, Daniel Kroetz, Martin Weiss, Mathieu Desrosier, Jason Karamchandani, Amit Bar-Or, Ted Fon, John Brietner, Derek Lo, Patrick Bermudez, Chris Steele, Pamela Patterson and one of my favourites: Pierre Bellec!

LORIS team on left (special thanks to Christine Rogers for listening to me.)