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OpenNeuro: a free online platform for sharing and analysis of neuroimaging data

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Organization for Human Brain Mapping 2017

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OpenNeuro: a free online platform for sharing and analysis of neuroimaging data

  1. 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. 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. 3. OpenNeuro.org - Poster #1677 3
  4. 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. 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. 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. 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. 8. OpenNeuro.org - Poster #1677 8
  9. 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. 10. Demo OpenNeuro.org - Poster #1677 10
  11. 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. 12. Under the hood OpenNeuro.org - Poster #1677 12
  13. 13. BIDS Apps OpenNeuro.org - Poster #1677 13 Gorgolewski et al. 2017
  14. 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. 15. OpenNeuro.org - Poster #1677 15
  16. 16. Reproducibility Data snapshots + software containers == reproducibility OpenNeuro.org - Poster #1677 16
  17. 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. 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. 19. Want to deploy your workflow on OpenNeuro? Get in touch! OpenNeuro.org - Poster #1677 19
  20. 20. OpenNeuro.org - Poster #1677 20 Poldracklab bids-apps.neuroimaging.org

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