toward an open ecosystem for neuroimaging meta-analysis courses/course... · voxelwise encoding...
TRANSCRIPT
poldracklab.org
Toward an open ecosystem for neuroimaging meta-analysis
Russell Poldrack
Department of Psychology
Stanford University
# of
Pub
Med
abs
tract
s m
entio
ning
fMR
I
# of
Pub
Med
abs
tract
s m
entio
ning
fMR
I
How much of this data is accessible to us?
# of
Pub
Med
abs
tract
s m
entio
ning
fMR
I
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
poldracklab.org
What does “open” mean?
• Minimal intellectual property restrictions
https://creativecommons.org/choose/zero/
poldracklab.org
What does “open” mean?
• Programmatically accessible via web API
http://neurovault.org/api-docs
poldracklab.org
What does “open” mean?
• Programmatically accessible via web API
http://neurovault.org/api/atlases/
poldracklab.org
Neurosynth.org
poldracklab.org
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
poldracklab.org
Towards image-based meta-analysis
vs
108 bytes
1.7 MB
poldracklab.org
Neurovault: Sharing statistical maps
Gorgolewski et al., 2015
Poster #1951
poldracklab.org
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
poldracklab.org
Instant sharing using SPMSPM export to NIDM-Results
.nidm
.zip
courtesy of Guillaume Flandin
poldracklab.org
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
poldracklab.org
OpenfMRI: Sharing complete raw datasets
• Fully open sharing • No restrictions on data access/usage • CC0 license
poldracklab.org
Open standards: Brain Imaging Data Structure (BIDS)
http://bids.neuroimaging.iohttp://incf.github.io/bids-validator/
poldracklab.org
Getting the openfmri data
poldracklab.org
Programmatic access to OpenfMRI data
poldracklab.org
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
poldracklab.org
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.
poldracklab.org
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
poldracklab.org
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
poldracklab.org
Toward an open annotated ecosystem
poldracklab.org
Ontology-enabled meta-analysis
lexical decision task
word vs. nonword
story memory task
related vs. unrelated
Cognitive processes Cognitive tasks Data
poldracklab.org
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
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
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
poldracklab.org
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
poldracklab.org
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