poldracklab.org

Toward an open ecosystem for neuroimaging meta-analysis

Russell Poldrack

Department of Psychology

Stanford University

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How much of this data is accessible to us?

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How much of this data is accessible to us?

poldracklab.org

An open ecosystem for neuroimaging meta-analysis

Brea

dth

Depth

Coordinates

Statistical maps

Full raw datasets

poldracklab.org

An open ecosystem for neuroimaging meta-analysis

Brea

dth

Depth

Statistical maps

Full raw datasets

poldracklab.org

An open ecosystem for neuroimaging meta-analysis

Brea

dth

Depth

Full raw datasets

poldracklab.org

An open ecosystem for neuroimaging meta-analysis

Brea

dth

Depth

poldracklab.org

An open ecosystem for neuroimaging meta-analysis

Brea

dth

Depth

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What does “open” mean?

• Minimal intellectual property restrictions

https://creativecommons.org/choose/zero/

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What does “open” mean?

• Programmatically accessible via web API

http://neurovault.org/api-docs

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What does “open” mean?

• Programmatically accessible via web API

http://neurovault.org/api/atlases/

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Neurosynth.org

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Neurosynth as an open resource

• All data and source code are freely available online

• Data are released under Open Database License (ODbL)

• Code released under permissive MIT license

• Web API:

• http://neurosynth.org/api/v2/

• Python package:

• https://github.com/neurosynth/neurosynth

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Towards image-based meta-analysis

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1.7 MB

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Neurovault: Sharing statistical maps

Gorgolewski et al., 2015

Poster #1951

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Allen Human Gene Expression Atlas

• An "all genes, all structures" gene expression survey in 6 adult human brains

• > 62,000 gene probes per profile

• ~ 500 samples per hemisphere across cerebrum, cerebellum and brainstem

• Data mapped with histology into unified 3-D anatomic framework based on MRI

http://human.brain-map.org/microarray/search

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Instant sharing using SPMSPM export to NIDM-Results

.nidm

.zip

courtesy of Guillaume Flandin

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Neurovault as an open resource

• Open access to code and data

• Data released under CC0 license

• Source code released under unrestrictive MIT license

• Data mirrored on Stanford Digital Repository for longevity

• Web API offers programmatic access to database

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OpenfMRI: Sharing complete raw datasets

• Fully open sharing • No restrictions on data access/usage • CC0 license

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Open standards: Brain Imaging Data Structure (BIDS)

http://bids.neuroimaging.iohttp://incf.github.io/bids-validator/

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Getting the openfmri data

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Programmatic access to OpenfMRI data

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OpenfMRI reuse statistics

• 173 reuses as of March 2017

• Estimated value of reuse: $2,955,588

Gorgolewski et al., 2015, OHBM,

Wexler et al, 2017, unpublished

openneuro.org

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Annotating the data

• Task metadata

• “What happened when during the task?”

• Annotation

• “What psychological processes were engaged by each condition in the task?”

Poldrack et al., 2011, Frontiers in Neuroinformatics

Mental Conceptsexecutive function

Response inhibition

Working memory updating Set shifting

is-ais-ais-a

Task set reconfiguration

Response suppression

part-ofpart-of

precedes

part-of

cognitive control has-synonym

Mental Tasks

Stop-signal task

Stop trial

Go trial

Experimental conditions Contrasts

SSRT

Response time

Indicators

Accuracy

Mean Go RT

has-condition

has-condition

Choice RTtask

derived-from

is-measured-by

Response inhibition

Suppression of actions that are inappropriate in a given context and that interfere with goal-driven behavior.

BibliographyLogan, G. D. & Cowan, W. B. (1984). On the ability to inhibit thought and action: A theory of an act of control. Psychological Review, 91, 295-327.

Stop-signal task

A task in which an external stimulus signals the participant to interrupt an already-initiated motor response.

BibliographyVerbruggen, F., & Logan, G. D. (2008). Response inhibition in the stop-signal paradigm. Trends in Cognitive Sciences, 12, 418-424.

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Current state of the Cognitive Atlas

• 806 mental constructs

• 737 tasks

• 220 disorders (inherited from Disease Ontology)

• web API

• python package: pip install cognitiveatlas

• Soon to be updated with new features

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Cognitive Atlas annotation of neurovault data

Cognitive Atlas

Balloon Analog Risk Task

has-contrast

Pumps Parametric - Control Parametric

riskreward

anticipationresponse execution

measured-by

93 task contrasts annotated manually

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Toward an open annotated ecosystem

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Ontology-enabled meta-analysis

lexical decision task

word vs. nonword

story memory task

related vs. unrelated

Cognitive processes Cognitive tasks Data

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Voxelwise encoding model for cognitive processes

Voxel response(Z-score)

for each taskcontrast

=

Ontology encoding for each task contrast(expanded to include all parent terms)

x 𝛃

Weighting for each ontology

element

Estimate 𝝱 using regularized regression (elastic net)

cognitive processes

task

con

trast

s

Sochat et al., in prep

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Predicting activation maps from cognitive processes

Train encoding model at

each voxel(leave-2-out)

Test set (2 images)

𝛃voxelpred = X*𝛃voxel

Predicted images

Actualimages

r1,1 r1,2 r2,2r2,1Success:r1,1 > r1,2r2,2 > r2,1

Sochat et al., in prep

poldracklab.org

Predicting activation maps from cognitive processes

Train encoding model at

each voxel(leave-2-out)

Test set (2 images)

𝛃voxelpred = X*𝛃voxel

Predicted images

Actualimages

r1,1 r1,2 r2,2r2,1Success:r1,1 > r1,2r2,2 > r2,1

Sochat et al., in prep

• 81% correct

• p<.001 vs null model

• Without ontology expansion:

• 56% correct

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Conclusions

• Everyone benefits when we share things openly

• Minimally restrictive licensing maximizes access to data resources

• Maximizes the benefits from our subjects’ participation

• Programmatic access to data and knowledge resources will enable new kinds of automated meta-analysis

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AcknowledgmentsJeanette Mumford Sarah Helfinstein Tom Schonberg Craig Fox Koji Jimura Sanmi Koyejo Chris Gorgolewski Tyler Davis Tal Yarkoni Jessica Cohen Robert Bilder Eliza Congdon Eydie London Tyrone Cannon Nelson Freimer Stephen J. Hanson Yaroslav Halchenko The Poldrack Lab @ Stanford

James S. McDonnell Foundation

http://reproducibility.stanford.edu