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ML Researcher’s Guide to Open Brain Imaging Data

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Presentation given at HealthAI kickoff meeting https://health-ai.github.io/

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ML Researcher’s Guide to Open Brain Imaging Data

  1. 1. ML RESEARCHER’S GUIDETO OPEN BRAIN IMAGING DATA Chris Gorgolewski @ChrisFiloG Stanford Center for Reproducible Neuroscience
  2. 2. WHY BRAIN DATA IS IMPORTANT?
  3. 3. The cost of mental health
  4. 4. The end of radiology? “People should stop training radiologists now” Jeff Hinton, 2016 https://www.youtube.com/watch?v=2HMPRXstSvQ
  5. 5. algorithms + data = breakthroughs https://www.kdnuggets.com/2016/05/datasets-over-algorithms.html
  6. 6. THE NATURE OF THE DATA
  7. 7. 3D cubes of values
  8. 8. Structural scans ■ Single 3D image ■ “high resolution“ 256x256x160 ■ Different histogram profiles
  9. 9. Diffusion scans ■ Series (x70-90) of 3D images – Each with slightly different contrast ■ Good for looking at white matter – axons – “wiring of the brain”
  10. 10. Functional scans ■ Long series of seemingly identical images ■ Low resolution 64x64x64x600 ■ Sensitive to tiny differences in blood flow ■ Can detect which parts of the brain are “active” at any given time ■ Great for studying cognition
  11. 11. EXISTING RESOURCES
  12. 12. Brain tumors T1 T2 diffusion functional Pernet dataset • 22 participants • T1,T2, diffusion, functional • Demographics • Photographs from surgeries https://www.nature.com/articles/sdata20163
  13. 13. Brain tumors BRATS • 30 participants • T1,T2, FLAIR, and post- GadoliniumT1 • Segmented • Designed for a MICCAI competition http://www2.imm.dtu.dk/projects/BRATS2012/data.html
  14. 14. Brain tumors BITE: Brain Images of Tumors for Evaluation database • 15 participants • T1-weighted MR with gadolinium • Ultrasound images • Pre and post resection http://nist.mni.mcgill.ca/?page_id=672
  15. 15. Stroke ATLAS (Anatomical Tracings of LesionsAfter Stroke) • 304 participants • T1-weighted • Manually segmented https://www.nature.com/articles/sdata201811
  16. 16. Alzheimer’s Disease Neuroimaging Initiative (ADNI) ■ T1,T2, functional, diffucion and PET data ■ Longitudinal ■ ~800 participants http://adni.loni.usc.edu/
  17. 17. Autism Brain Imaging Data Exchange (ABIDE) ■ 2156 participants ■ T1 and functional data ■ Phenotypic data http://fcon_1000.projects.nitrc.org/indi/abide
  18. 18. Attention Deficit Hyperactivity Disorder 200 ■ 776 participants ■ T1w and functional ■ Part of a competition http://fcon_1000.projects.nitrc.org/indi/adhd200/
  19. 19. OASIS-3: Longitudinal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and Alzheimer’s Disease ■ 1098 participants – 609 cognitively normal adults – 489 individuals at various stages of cognitive decline ■ T1w,T2w, FLAIR, ASL, SWI, time of flight, resting-state BOLD, and DTI sequences http://www.oasis-brains.org
  20. 20. SchizConnect ■ 1302 participants ■ Aggregated data across sites ■ T1,T2, functional http://schizconnect.org/
  21. 21. Transfer learning Catalog of healthy structural brain scans: github.com/cMadan/openMorph ~100,000T1 scans
  22. 22. Brainhack Global San Francisco ■ San Francisco, CA, USA ■ May 03-05, 2018 ■ https://sfbrainhack.github.io/ ■ Friendly vibes, local experts willing to collaborate
  23. 23. Got stuck? http://neurostars.org open online Q/A community for neuroimaging

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