Applying FreeSurfer Tools to FSL fMRI Analysis 1 Integrating FreeSurfer and FSL FEAT.
· SPM Guillaume Flandin. FSL Mark Jenkinson, Matthew Webster, Paul McCarthy, Eugene Duff, FSL...
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Transcript of · SPM Guillaume Flandin. FSL Mark Jenkinson, Matthew Webster, Paul McCarthy, Eugene Duff, FSL...
Analysis
Pre-processing
Publication
Raw data
Pre-processed data
Results
Publication
Publicly available
data
Analysis
Pre-processing
Publication
Raw data
Pre-processed data
Results
Publication
Publicly available
data
Analysis
Pre-processing
Publication
Raw data
Pre-processed data
Results
Publication
< 5% of data shared in public repositoriesB
UT
Analysis
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Analysis
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Publication
Peak locationsFigure
(selected slices)Thresholded
statistics
Analysis
Pre-processing
Publication
Raw data
Pre-processed data
Results
Publication
Publication
Peak locationsFigure
(selected slices)Thresholded
statistics
Analysis
Pre-processing
Publication
Raw data
Pre-processed data
Results
Publication
❌❌❌
Analysis
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Pre-processed data
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Study 1
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Study 2
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Study n...
Meta-analysisResults
Coordinate- or Image-Based?Acquisition Analysis
Experiment Raw data Results
Acquisition Analysis
Experiment Raw data Results
…
Publication
Publication
Paper
Paper
Coordinate- or Image-Based?Acquisition Analysis
Experiment Raw data Results
Acquisition Analysis
Experiment Raw data Results
…
Publication
Publication
Paper
Paper
Coordinate-based meta-analysis
Coordinate-based meta-analysis
Image-based meta-analysis
Shared results
Full results reporting
Coordinate- or Image-Based?Acquisition Analysis
Experiment Raw data Results
Acquisition Analysis
Experiment Raw data Results
…
Publication
Publication
Paper
Paper
Coordinate-based meta-analysis
Coordinate-based meta-analysis Image-based meta-analysis
Standard error map
Statistic mapE.g. Z-map
Contrast map Design matrix(png and csv)
NIDM-Resultsgraph
.nidm
.zip
http://nidm.nidash.org/specs/nidm-results.html
Definition
Attributes
Examples
Harmonisation across software
• Model of the error– Prob. distribution:– Variance:
– Dependence:heterogeneous
Independent noise
homogeneous
Compound Symmetry
Serially correlated
Arbitrarily correlated
Gaussian Non-Parametric …
global
local
regularized
Error models: SPM, FSL and AFNIGroup levelSubject level
$ nidmfsl ds107.gfeat -g Control 49
pip
https://github.com/incf-nidash/nidmresults-fslhttp://fsl.fmrib.ox.ac.uk
Coordinate-based meta-analysis Image-based meta-analysis
Scripts available at http://github.com/incf-nidash/nidmresults-paper
Thank you! To all the INCF NIDASH task force members.
This work is supported by the
Warwick neurodata sharing Tom Nichols, Alex Bowring, Ruth Pauli, Peter Williams, Tom Maullin-Sapey.
NIDM working group Tibor Auer, Samir Das, Fariba Fana, Guillaume Flandin, Satra Ghosh, Tristan Glatard, Chris Gorgolewski, Karl Helmer, David Keator, Nolan Nichols, Jean-Baptiste Poline, Vanessa Sochat, Jason Steffener, Jessica Turner.
SPM Guillaume Flandin.FSL Mark Jenkinson, Matthew Webster, Paul McCarthy, Eugene Duff, FSL Steve Smith.AFNI Gang Chen, Richard Reynolds, Ziad Saad, Robert Cox.
Meta-analysis dataset Tracey group at FMRIB.
Q & A
Maumet, C. et al. Sharing brain mapping statistical results with the neuroimaging data model. Sci. Data 3:160102 doi: 10.1038/sdata.2016.102 (2016).
https://github.com/incf-nidash http://nidm.nidash.org
