Due to the lack of data shared when reporting neuroimaging results, most neuroimaging meta-analyses are based on peak coordinate data. However, the best practice is an image-based meta-analysis that combines full image data of the effect estimates and standard errors derived from each study.
The Neuroimaging Data Model (NIDM) is an ongoing effort, supported by the INCF, to provide a domain-specific extension of the W3C PROV-DM.
In this talk, I will review our recent progress in extending NIDM to share the statistical results of a neuroimaging study and our interactions with existing software packages (SPM, FSL, AFNI, Neurovault.org).
5. 5
International Neuroinformatics
Coordinating Facility
Program on Digital
Brain Atlasing
2 Task Forces
– Neuroimaging (NIDASH)
– Electrophysiology
6. NIDM working group
• NIDASH Task force
– “Standards for Data Sharing aims to develop
generic standards and tools to facilitate the
recording, sharing, and reporting of
neuroscience metadata, in order to improve
practices for the archiving and sharing of
neuroscience data.”
• BIRN Derived Data Working Group
6
7. From XCEDE to NIDM
• XML-Based Clinical Experiment Data
Exchange Schema (XCEDE): www.xcede.org
– Describes subject, study, activation
– Limited provenance encoding
– Initiative of the BIRN
• XCEDE-DM
• NeuroImaging Data Model (NIDM):
www.nidm.nidash.org
7
9. NIDM: Neuroimaging Data Model
• Based on PROV-DM
• First applications
– Description of the dataset-experiment hierarchy
– Freesurfer volumes
– DICOM terms
9
11. Why meta-analyses?
Data
acquisition Analysis
Experiment Raw data Results
Data
acquisition Analysis
…
Experiment Raw data Results
• Increase statistical power
• Combine information across studies
Results
Meta-analysis
11
12. Data analysis in neuroimaging
Analysis
Data
acquisition
Experimen t Results
Publication
Raw data Paper
Imaging
data
12
500MB/subject
0MB < 0.5MB
20GB
2.5GB/subject
100GB
[ ~2GB for stats]
13. Data analysis in neuroimaging
Table of local maxima
(quantitative)
13
Paper
Publication
?
Detection images
(qualitative)
Peaks
(quantitative)
< 0.5MB
14. Coordinate- or Image-Based meta-analysis?
14
Data
acquisition Analysis
Experiment Raw data Results
Data
acquisition Analysis
…
Experiment Raw data Results
Publication
Publication
Paper
Paper
Coordinate-based
meta-analysis
Image-based
meta-analysis
Shared results
Data sharing
17. Three major software packages
17
~80%
Automatically created with Neurotrends based on over
16 000 journal articles; Source:
http://neurotrends.herokuapp.com/static/img/temporal/pkg-prop-year.png
18. Summary of the problem
• Use-case: Support meta-analysis
• Machine-readable format describing
neuroimaging results
• Easiness for the end-user
• Integrate with existing neuroimaging software
packages (SPM, FSL, AFNI,…)
• Extend previous work: NIDM
18
26. Standardization across software
• Model of the error
– Prob. distribution:
– Variance:
– Dependence:
26
Gaussian
Non-‐Parametric
heterogeneous
Independent
noise
homogeneous
Compound
Symmetry
Serially
correlated
Arbitrarily
correlated
…
global
local
regularized
27. Error models : SPM, FSL and AFNI
27
1st level 2nd level
Gaussian
Serial.
corr.
global
Homogeneous
local
Gaussian
Independent
noise
Homogeneous
local
Gaussian
Homogeneous
local
Serial.
corr.
regularized
Gaussian
Homogeneous
local
Serial.
corr.
local
Gaussian
Independent
noise
Heterogeneous
local
Gaussian
Independent
noise
Hetero-‐
or
Homogeneous
local
28. Error models: non-parametric
28
2nd level: Sign-flipping
Heterogeneous
local
Independent
noise
NonParametric
Symmetric
2nd level: Label permutation
Homogeneous
local
Exchangeable
noise
local
NonParametric
29. Terms
• “Flat” ontology
• Terms re-use:
– Interaction with STATO (statistical terms)
– Dublin Core (file formats)
– But also: NCIT, OBI…
• Work-in-progress
• http://tinyurl.com/nidm-results/terms
• Aim: include the terms in Neurolex.
29
30. Queries
• For each contrast get name, contrast file,
statistic file and type of statistic used.
30
prefix
prov:
<http://www.w3.org/ns/prov#>
prefix
nidm:
<http://www.incf.org/ns/nidash/nidm#>
SELECT
?contrastName
?contrastFile
?statType
?statFile
WHERE
{
?cid
a
nidm:ContrastMap
;
nidm:contrastName
?contrastName
;
prov:atLocation
?contrastFile
.
?cea
a
nidm:ContrastEstimation
.
?cid
prov:wasGeneratedBy
?cea
.
?sid
a
nidm:StatisticMap
;
nidm:statisticType
?statType
;
prov:atLocation
?statFile
.
}
More queries: http://tinyurl.com/nidm-results/query
34. Next steps and future plans
• Extend NIDM-Results implementation:
– AFNI
– SnPM, Randomise
• Refine the terms and definitions.
34
35. Next steps and future plans
• NIDM import for
Neurovault
35
36. NIDM-Results and NIDM-Workflow
• NIDM-Results: effort on standardization
across software
– A small number of generic activities
– A few software-specific entities
• NIDM-Workflow: a detailed view of all
software-specific processes.
36
40. Acknowledgements
40
Thank you! To all the INCF
NIDASH task force members.
NIDM working group
Tibor Auer, Gully Burns, Fariba Fana, Guillaume Flandin, Satrajit Ghosh,
Chris Gorgolewski, Karl Helmer, David Keator, Camille Maumet,
Nolan Nichols, Thomas Nichols, Jean-Baptiste Poline, Jason Steffener,
Jessica Turner.
INCF NIDASH - Other members
David Kennedy, Cameron Craddock, Stephan Gerhard,
Yaroslav Halchenko, Michael Hanke, Christian Haselgrove, Arno Klein,
Daniel Marcus, Franck Michel, Simon Milton, Russell Poldrack,
Rich Stoner.
This work is supported by the