Organization for Human Brain Mapping 2017

1. Krzysztof J. Gorgolewski, Oscar Esteban, Gunnar Schaefer,
Brian A. Wandell, and Russell A. Poldrack
a free online platform for sharing and
analysis of neuroimaging data

2. MR Data Analysis - theory
1. Perform quality control
2. Develop a pipeline
3. Run the pipeline
4. Share the data
OpenNeuro.org - Poster #1677 2

3. OpenNeuro.org - Poster #1677 3

4. MR Data Analysis - theory
1. Perform quality control
2. Develop a reproducible pipeline
3. Run the pipeline
4. Share the data
OpenNeuro.org - Poster #1677 4

5. MR Data Analysis - reality
1. Perform quality control
• Too much work to look at all images. I’m sure it’s perfect.
2. Develop a reproducible pipeline
• Limited to tools I know, reproducibility too difficult.
3. Run the pipeline
• Let’s skip running FreeSurfer, takes too much time on my laptop.
4. Share the data
• So what do I gain from this?
OpenNeuro.org - Poster #1677 5

6. MR Data Analysis - vision
1. Perform quality control
2. Develop a reproducible pipeline
3. Run the pipeline
4. Share the data
OpenNeuro.org - Poster #1677 6

7. What is OpenNeuro?
• Science as a Service platform
• Similar to CBRAIN, MRI Cloud, Mint, and Flywheel
• Evolution of OpenfMRI.org
• Upload, manage, and share your data
• Based on Brain Imaging Data Structure
• Immutable dataset snapshots
OpenNeuro.org - Poster #1677 7

8. OpenNeuro.org - Poster #1677 8

9. What is OpenNeuro?
• Science as a Service platform
• Similar to CBRAIN, MRI Cloud, Mint, and Flywheel
• Evolution of OpenfMRI.org
• Upload, manage, and share your data
• Based on Brain Imaging Data Structure
• Immutable dataset snapshots
• Run predefined analyses – Apps
• Based on BIDS Apps framework
• Each workflow captured in a software container
OpenNeuro.org - Poster #1677 9

10. Demo
OpenNeuro.org - Poster #1677 10

11. Available Pipelines
• FMRIPREP
• MRIQC
• C-PAC
• FreeSurfer
• ndmg
• SPM
Coming soon:
• QAP
• OPPNI
• automatic analysis
• MAGeTBrain
• TRACULA
• BROCCOLI
• BARACUS
OpenNeuro.org - Poster #1677 11

12. Under the hood
OpenNeuro.org - Poster #1677 12

13. BIDS Apps
OpenNeuro.org - Poster #1677 13
Gorgolewski et al. 2017

14. Open Source
• All platform components are open source and
reusable:
• Embeddable BIDS Validator
• BIDS Apps
• Frontend
• AWS based execution engine
github.com/poldracklab
github.com/BIDS-Apps
OpenNeuro.org - Poster #1677 14

15. OpenNeuro.org - Poster #1677 15

16. Reproducibility
Data snapshots + software containers
==
reproducibility
OpenNeuro.org - Poster #1677 16

17. Incentive for sharing data
OpenNeuro is free to use by anyone
under the agreement that the data will be made
publicly available after 18 months.
OpenNeuro.org - Poster #1677 17

18. Future direction
• Running apps on outputs of other apps
• Higher level analyses
• More computational backend
• CBRAIN
• OSG
• XSEDE
OpenNeuro.org - Poster #1677 18

19. Want to deploy your workflow on
OpenNeuro?
Get in touch!
OpenNeuro.org - Poster #1677 19

20. OpenNeuro.org - Poster #1677 20
Poldracklab
bids-apps.neuroimaging.org