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

1. ML RESEARCHER’S
GUIDETO OPEN BRAIN
IMAGING DATA
Chris Gorgolewski
@ChrisFiloG
Stanford Center for Reproducible Neuroscience

2. WHY BRAIN DATA
IS IMPORTANT?

3. The cost of mental health

4. The end of radiology?
“People should stop training
radiologists now”
Jeff Hinton, 2016
https://www.youtube.com/watch?v=2HMPRXstSvQ

5. algorithms + data = breakthroughs
https://www.kdnuggets.com/2016/05/datasets-over-algorithms.html

6. THE NATURE
OF
THE DATA

7. 3D cubes of values

8. Structural scans
■ Single 3D image
■ “high resolution“ 256x256x160
■ Different histogram profiles

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. 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. EXISTING
RESOURCES

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. 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. 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. Stroke
ATLAS (Anatomical
Tracings of LesionsAfter
Stroke)
• 304 participants
• T1-weighted
• Manually segmented
https://www.nature.com/articles/sdata201811

16. Alzheimer’s Disease
Neuroimaging Initiative (ADNI)
■ T1,T2, functional,
diffucion and PET data
■ Longitudinal
■ ~800 participants
http://adni.loni.usc.edu/

17. Autism Brain Imaging Data
Exchange (ABIDE)
■ 2156 participants
■ T1 and functional data
■ Phenotypic data
http://fcon_1000.projects.nitrc.org/indi/abide

18. Attention Deficit
Hyperactivity Disorder 200
■ 776 participants
■ T1w and functional
■ Part of a competition
http://fcon_1000.projects.nitrc.org/indi/adhd200/

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. SchizConnect
■ 1302 participants
■ Aggregated data
across sites
■ T1,T2, functional
http://schizconnect.org/

21. Transfer learning
Catalog of
healthy structural brain scans:
github.com/cMadan/openMorph
~100,000T1 scans

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. Got stuck?
http://neurostars.org
open online Q/A community for
neuroimaging