supporting image-based meta-analysis with nidm: standardized reporting of neuroimaging results
DESCRIPTION
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).TRANSCRIPT
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University of Warwick, Neuroimaging Statistics, Coventry, UK.
Camille Maumet
Supporting image-based meta-analysis with NIDM: Standardized reporting of neuroimaging results
INCF NIDASH Task force
Oct. 8th 2014
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Agenda
• Context – NIDM and the INCF NIDASH Task force – Meta-analysis use-case – Data sharing environment
• NIDM for meta-analysis – NIDM-Results – Implementation – Future directions
• Conclusions
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CONTEXT
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INCF NIDASH Task Force CONTEXT
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International Neuroinformatics Coordinating Facility
Program on DigitalBrain Atlasing
2 Task Forces – Neuroimaging (NIDASH) – Electrophysiology
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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
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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
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NIDM: Neuroimaging Data Model
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Source: Poline et al, Frontiers in Neuroinformatics (2012).
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NIDM: Neuroimaging Data Model
• Based on PROV-DM • First applications
– Description of the dataset-experiment hierarchy – Freesurfer volumes – DICOM terms
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Meta-analysis use case CONTEXT
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Results
Meta-analysis
Results
Results
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Why meta-analyses?
• Increase statistical power • Combine information across studies
Data acquisition Analysis
Experiment Raw data Results
Data acquisition Analysis
Experiment Raw data Results
… Results
Meta-analysis
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Data analysis in neuroimaging Analysis
Results Experiment
Data acquisition
Raw data Paper
Publication
MRI acquisition parameters
Task design and timing
Description of
participants
Mental processes
studied
Imaging data
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500MB/subject 20GB
2.5GB/subject 100GB
[ ~2GB for stats]
< 0.5MB 0MB
Data processing and analysis procedure
Meta data
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Data analysis in neuroimaging
Table of local maxima (quantitative)
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Paper
Publication
?
Detection images (qualitative)
Peaks (quantitative)
< 0.5MB
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Coordinate- or Image-Based meta-analysis?
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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
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Data sharing environment CONTEXT
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Acquisition
Pre-processing
Statistical analysis
Data sharing tools
Publication
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Three major software packages
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Automatically created with Neurotrends based on over 16 000 journal articles; Source: http://neurotrends.herokuapp.com/static/img/temporal/pkg-prop-year.png
~80%
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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
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NIDM FOR META-ANALYSIS
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NIDM-Results NIDM FOR META-ANALYSIS
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Neuroimaging Data Model
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NIDM-Results
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NIDM-Results
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NIDM-Results: SPM-specific
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NIDM-Results: FSL-specific
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Standardization across software
• Model of the error – Prob. distribution: – Variance:
– Dependence:
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heterogeneous
Independent noise
homogeneous
Compound Symmetry
Serially correlated
Arbitrarily correlated
Gaussian Non-‐Parametric …
global
local
regularized
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Error models : SPM, FSL and AFNI
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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
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Error models: non-parametric
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2nd level: Sign-flipping
Heterogeneous local
Independent noise
NonParametric Symmetric
2nd level: Label permutation
Homogeneous local
Exchangeable noise local
NonParametric
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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.
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Queries • For each contrast get name, contrast file,
statistic file and type of statistic used.
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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
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Implementation NIDM FOR META-ANALYSIS
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Implementation
• NIDM export – SPM12 (natively) – Scripts for FSL:
https://github.com/incf-nidash/nidm-results_fsl – First contact with AFNI developers
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Future directions NIDM FOR META-ANALYSIS
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Next steps and future plans
• Extend NIDM-Results implementation: – AFNI – SnPM, Randomise
• Refine the terms and definitions.
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Next steps and future plans • NIDM import for
Neurovault
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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.
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CONCLUSION
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Conclusion
• NIDM-Results: standardized reporting of neuroimaging results – Use-case: Meta-analysis – Terms: http://tinyurl.com/nidm-results/terms/ – Specification: http://nidm.nidash.org – Implementation in SPM12 & FSL
• Next steps – Refine the terms, AFNI and SnPM/Randomise models – Integration with Neurovault – Build apps
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Resources • Github: https://github.com/incf-nidash • Specifications: http://nidm.nidash.org
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Acknowledgements
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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
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Q & A
• Github: https://github.com/incf-nidash • Specifications: http://nidm.nidash.org
NIDM Resources