Part of "The Big Data to Knowledge (BD2K) Guide to the Fundamentals of Data Science"

1. Avoiding the Tower
of Babel
The Role of Data Description Standards in
Biomedical Imaging
Chris Gorgolewski
Stanford University
@ChrisFiloG
The Big Data to Knowledge (BD2K)
Guide to the Fundamentals of Data Science

2. Chris Gorgolewski
• Obtained Ph.D. degree from University of Edinburgh, 2013
• Co-director of the Stanford Center for Reproducible Neuroscience
• Research involves building tools to enable researchers to efficiently share
their data, run reproducible analyses & link the results with previously reported
findings.
• Promotes data sharing through initiatives such as data papers & NeuroVault.
• Core developer of neuroimaging data processing framework Nipype, fMRI
preprocessing tool FMRIPREP, & quality control tool MRIQC
• Coordinator of the Brain Imaging Data Structure (BIDS) standard.
• http://chrisgorgolewski.org

3. What are standards useful for?

4. Standardy to forma jezyka
Standardy to sposob komunikacji.
Jezeli nie zanalibysmy wspolnego jezyka
nie bylibysmy sie wstanie komunikowac
i wspolnie budowac wielkich rzeczy.

5. Standards are a language
Standards are a way of communicating.
Without knowing the language we speak
we would not be able to communicate
and build great things.

6. Esperanto!
• Artificial language
• Created in 1870
• Optimized for ease of learning

7. Computer ports

8. Computer ports - ambiguity
USB C vs
Thunderbolt 3 vs
DisplayPort

9. Electricity

10. Digital communication
The Internet is possible
because of standards:
• DNS
• IP
• HTTP
• SMTP

11. Application Programmatic Interfaces (APIs)
• Building blocks of
Web 2.0
• Enable rapid
prototyping and
flexible scaling

12. How standards are developed in
the industry?

13. Institute of Electrical and Electronics
Engineers (IEEE)
802.11 aka Wi-Fi

14. Institute of Electrical and Electronics
Engineers (IEEE)

15. World Wide Web Consortium (W3C)

16. World Wide Web Consortium (W3C)

17. National Electrical Manufacturers Association
(NEMA)
Digital Imaging and
Communications in
Medicine (DICOM)

18. How standards are developed in
academia?

19. How to look for standards? FAIRSharing.org

20. Standards in academia
• Bottom up
• Often developed for a specific project (CIFTI, XCEDE, OpenfMRI)
• Technically simple
• Competitive (NIFTI vs. MINC)
• When widely adopted can be of great value (NIFTI)

21. Use case:
Brain Imaging Data Structure

22. Goals
• Enable reuse of research neuroimaging data
• Shared within or between labs
• Enable automatic analysis of datasets
• No need to manually input scanning parameters
• Make automatic consistency validation of datasets
possible
• In context of public data sharing

23. Consumers
• Lab PIs
• To reduce errors in data handling
• To enable reuse of data within your own lab
• Pipeline developers
• To enable automatic data processing
• Databases and repositories
• To enable automatic data submission

24. Meet Prof. Smith
POSTER NUMBER:
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25. Meet Mike
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26. Getting lost in your data
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27. Keys to success
• Involve broad scientific community
• Step outside of the bubble of your own lab
• Share the credit
• Let it be a truly collaborative – not just a product of your lab
• Focus on the use cases
• Make public call for comments
• Follow 80/20 rule
• Provide tools (validator)

28. Community! Community! Community!

29. Ways to get more people involved
• Ease the barrier to provide feedback
• Fully open mailing list
• Online Google Doc open for anyone to comment (even anonymously)
• Give credit
• List contributors by name
• Induce the feeling of shared ownership
• Acknowledge all types of contributions
• Organize in person meetings
• Dedicated workshops or along conferences
• Be persistent!
• Most people will be too busy to help you out

30. Folder organization
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31. Folder organization
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32. Folder organization
participant_id age sex
sub-001 34 M
sub-002 12 F
sub-003 33 F
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33. Folder organization
NIfT
I
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34. Folder organization
{
"RepetitionTime": 3.0,
"EchoTime": 0.03,
"FlipAngle": 78,
"SliceTiming": [0.0, 0.2, 0.4, …],
"MultibandAccellerationFactor": 4,
"PhaseEncodingDirection": "j-"
}
POSTER NUMBER:
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35. Tools
APIs:
• Querying BIDS datasets programmatically
Converters:
• From scanner to data
Validators:
• Verifying dataset consistency

36. The Validator
incf.github.io/bids-validator/
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37. Decision making process for extensions
Proposal
• Initial draft written by experts
• Sent out for public comments
Refinement
• Creation of example datasets
• Implementing new functionality in the validator
Merge
• Striving for consensus
• Backwards compatibility

38. Extension examples
• Electroencephalography
• Positron Emission Tomography
• Intracranial Electroencephalography
• Multi spectral structural imaging
• Models
• Derived data
• Spetroscopy
Cyril Pernet
Melanie Ganz
Dora Hermes
Tal Yarkoni

39. Guiomar Niso

40. Use cases enabled by BIDS

41. BIDS Apps
Gorgolewski et al. 2017

42. Simple parallelization scheme – map/reduce

44. a free online platform for sharing and
analysis of neuroimaging data

45. Science as a Service architecture
OpenNeuro.org - Poster #1677 45

46. OpenNeuro.org - Poster #1677 46

47. Demo
OpenNeuro.org - Poster #1677 47

49. BIDS Contributors
• Tibor Auer 💬📖💡🔧📢
• Sylvain Baillet 📖🔍
• Elizabeth Bock 📖💡
• Eric Bridgeford 📖🔧
• Teon L. Brooks 📖💻
• Suyash Bhogawar 📖💡⚠️🔧💬
• Vince D. Calhoun 📖
• Alexander L. Cohen 🐛💻📖💬
• R. Cameron Craddock 📖📢
• Samir Das 📖
• Alejandro de la Vega 🐛💻⚠️
• Eugene P. Duff 📖
• Elizabeth DuPre 📖💡
• Eric A. Earl 🤔
• Anders Eklund 📖📢💻
• Guillaume Flandin 📖💻
• Satrajit S. Ghosh 📖💻
• Tristan Glatard 📖💻
• Mathias Goncalves 💻🔧📢
• Alexandre Gramfort 📖💡
• Yaroslav O. Halchenko 📖📢
• Thomas E. Nichols 📖
• Guiomar Niso 📖💡
• Robert Oostenveld 📖
• Dianne Patterson 📖
• John Pellman 📖
• Cyril Pernet 💬 📖 💡📋
• Dmitry Petrov 📖💻
• Russell A. Poldrack 📖🔍📢
• Jean-Baptiste Poline 📖📢🤔🎨
• Ariel Rokem 📖
• Gunnar Schaefer 📖
• Jan-Mathijs Schoffelen 📖
• Vanessa Sochat 📖
• Francois Tadel 📖🔌💡
• William Triplett 📖
• Jessica A. Turner 📖
• Joseph Wexler 📖💡
• Gaël Varoquaux 📖
• Daniel A. Handwerker 📖
• Michael Hanke 📖🤔🔧🐛📢
• Michael P. Harms 📖⚠️🔧
• Richard N. Henson 📖
• International Neuroinformatics Coordinating Facility 💵📋
• Mainak Jas 📖💻
• David Keator 📖
• Gregory Kiar 📖💻🎨🔧
• Laura and John Arnold Foundation 💵
• Xiangrui Li 📖💻
• Vladimir Litvak 📖
• Dan Lurie 🤔📖🔧🔌💻💬
• Camille Maumet 📖
• Christopher J. Markiewicz 💬📖💻
• Jeremy Moreau 📖💡
• Zachary Michael 📖
• Michael P. Milham 💡🔍
• National Institute of Mental Health 💵
• B. Nolan Nichols 📖

50. Resources
• IEEE Process: https://standards.ieee.org/develop/process.html
• W3C Process: https://www.w3.org/2017/Process-20170301/
• History of DICOM: https://link.springer.com/chapter/10.1007/978-3-
540-74571-6_4
• BIDS: https://www.nature.com/articles/sdata201644
• BIDS Apps:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcb
i.1005209
• Search for standards: https://fairsharing.org/

51. bids.neuroimaging.io
(specification, examples, discussion forum)
POSTER NUMBER:
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