Talk from OHBM education day 2018, an overview of data sharing and other resources for neuroimaging research. Also a brief discussion of the impact that openly shared data has had on publications.

1. Data sharing
repositories for
neuroimaging
research
Cameron Craddock, PhD
Computational Neuroimaging Lab
Associate Professor of Diagnostic Medicine
The University of Texas at Austin, Dell Medical School

2. Join the conversation:
https://sli.do
#OS1
Data for Oscar’s talk:
https://goo.gl/PRgMUL

3. Principles of Open Neuroscience
Data, tools and ideas should be openly shared
-The Neuro Bureau Manifesto
http://www.neurobureau.org

4. How does open science help?
• Democratizes access to tools, data, and info needed to
education next generation of researchers
• Provides computational researchers access to
connectomes data so that they can help to solve our
problems
• Quick way to amass the resources needed to test
hypotheses about brain function and dysfunction
• More efficient use of funding resources
• …

5. (Some) Data Repositories

6. The (re)beginning of sharing
neuroimaging data …
http://fcon_1000.projects.nitrc.org

7. INDI – more complete information
http://fcon_1000.projects.nitrc.org
• 35 different projects
• 10,192 participants, 98 non-human-primates
• T1, T2, qMRI, DTI, RfMRI, TfMRI, ASL, PET, EEG
• Prospective and retrospective data sharing
• Variety of phenotypes and assessments

8. Consortium Model
Data from 8 sites
Rest fMRI + SMRI
- 386 ADHD
- 535 Typical
Data from 27 sites
Rest fMRI + SMRI + DTI
- 1060 ADHD
- 1166 Typical
http://fcon_1000.projects.nitrc.org/indi/abide/
http://fcon_1000.projects.nitrc.org/indi/adhd200

9. Reproducibility and Reliability in
Connectomics
• Time between
scans varies from
minutes, days,
months
– 2 participants
scanned 5 times a
day for 3 days
– 1 participant
scanned 100
times
1,629 Healthy Controls
3,357 MRI scans
5,093 rs-fMRI scans
1,629 Diffusion scans
300 CBF scans
http://fcon_1000.projects.nitrc.org/indi/CoRR/html/index.html

10. Non-human Primate Consortium
• 25 international sites
• 98 animals
• sMRI, fMRI, DTI
• A variety of paradigms
– Anesthetized
– Awake
– Movie watching
http://fcon_1000.projects.nitrc.org/indi/indiPRIME.html

11. Beyond resting state …
• 122 distinct datasets
• 4056 unique
participants
• 208 different tasks
• sMRI, fMRI, PET, EEG,
MEG, DWI
is now
https://openneuro.org/

12. • One male scanned 107 times, 3
times a week
– T1, T2, DTI, resting state fMRI, task
fMRI
• Pre-prpocessed data available
• Blood sample once a week for
gene expression (via RNA
sequencing), metabolomics and
proteomic analyses, and others …
• blood pressure and weight
• foods eaten, alcohol intake, and
supplements/medicines taken
• exercise, time spent outdoors, and
physical soreness
• a free-text log of daily events
• Mood questionairre
• structured report of what the
subject was thinking about during
the resting state fMRI scan.
https://openneuro.org/ http://myconnectome.org

13. • 130 Controls, 50 schizophrenia, 49 bipolar, 43 ADHD
• T1-weighted Anatomical MPRAGE, 64 Direction DWI
• BOLD contrast fMRI
– Resting State (with physiological monitoring)
– Breath Hold fMRI (with physiological monitoring)
– Balloon Analog Risk Task (BART)
– Stop signal Task
– Task switching
– Spatial Working Memory Capacity Tasks (SCAP)
– Paired Associates Memory Task - Encoding/Retrieval
(PAMenc/PAMret)
• Preprocessed data available
http://www.phenomics.ucla.edu/index.asp
https://openneuro.org/datasets/ds000030/versions/00016

15. Centralized prospective data sharing

16. NKI Enhanced Rockland Sample
- Combined effort of 4 NIH R01
- Base – 1000 pts, 8 – 85 years old, community
based sample
- Child Longitudinal – 180 pts, 8 – 18 years old,
scanned 3x
- Neurofeedback – 200 pts, 21 – 45
- Adult Longitudinal – 40 – 85 years old, includes
cardiovascular fitness
- Base “connectomes” protocol
- Structural – T1, T2, FLAIR
- 128 direction DTI
- Resting state fMRI with various temporal and
spatial resolutions
- Perfusion (2D PCASL)
- Breath Holding http://fcon_1000.projects.nitrc.org/indi/enhanced/

17. Healthy Brain Network
Data from 10,000
Young people—
aged 5–21—across
the New York
metropolitan area
10,000 represents the
statistical magnitude
necessary to draw
reliable conclusions on
a dataset covering all
disorders
Data includes
Imaging data, including functional MRI measures and EEG
A broad range of psychiatric, behavioral, cognitive and lifestyle
information—clinical evaluations, IQ testing, family environment,
genetics, cardiovascular fitness and nutritional information
Builds on CMI Case Study in Open Science and Big Data:
The Rockland Sample
Since 2010, our scientists have been generating a database of
comprehensive assessments of 1,000 people, ages 6-85, to map the
brain across the lifespan and across the spectrum of mental illness.
79 published studies thus far (14 from CMI)
http://fcon_1000.projects.nitrc.org/indi/cmi_healthy_brain_network/index.html

18. HBN Extensive Assessment
http://fcon_1000.projects.nitrc.org/indi/cmi_healthy_brain_network/index.html

19. HBN EEG
• High density EEG (128 channels
geodesic hydrocel system
by EGI)
• Eye position and pupil dilation
are recorded concomitant with
EEG recordings,
http://fcon_1000.projects.nitrc.org
/indi/cmi_healthy_brain_network/
eeg_protocol.html

20. • Several datasets incorporating state of the art
connectome scanning, MEG, and assessments,
– Young Adult
– Lifespan (4 cohorts)
– A variety of disease populations (Alzheimer's, dementia,
epilepsy, anxiety, depression, psychosis, etc.)
• Preprocessed data available
https://www.humanconnectome.org

21. Processed data …

22. 1000 subjects, ~400 ADHD, 600
Typically Developing Children

23. ABIDE
Preprocessing
DPARSF
CBRAIN
CCS
http://preprocessed-connectomes-project.org/abide/

25. Manually Labeled Data
• 229 T1-weighted MRI
scans (n=220) with
manually segmented
lesions and metadata
The Neurofeedback Skull-
stripped (NFBS)
repository
• database of 125 T1-
weighted anatomical MRI
scans that are manually
skull-strippedhttp://preprocessed-connectomes-
project.org/NFB_skullstripped/index.ht
ml
http://fcon_1000.projects.nitrc.org/indi/retro/atlas.html

28. nitrc.org - Index of tools and data

30. http://bids.neuroimaging.io

31. http://bids-apps.neuroimaging.io

32. https://www.biorxiv.org/content/early/2017/09/04/183814
Between 2010 and 2016, 913 papers
published using INDI data!!

33. The benefits of sharing
https://www.biorxiv.org/content/early/2017/09/04/183814

34. Comparison with other literature