[pymvpa] Mixed effects and searchlight group significance thresholding

J.A. Etzel jetzel at artsci.wustl.edu
Mon Jul 9 19:59:47 UTC 2012

Group analysis for searchlight results is unfortunately not 
straightforward or agreed-upon. But a few thoughts, anyway.

First, I would not do small-volume corrections. This is mixing 
whole-brain (the searchlight) and ROI-based analyses/hypotheses. If you 
have a ROI-based hypothesis you should do ROI-based analyses (test the 
region directly); otherwise it's too easy to draw the ROIs around the 
blobs and create positive results out of anything.

Smoothing the single-subject maps then doing a 'normal' mass-univariate 
analysis in spm is a safer strategy, though as you point out, 
information maps are definitely not activation maps. I'd suggest trying 
something like whole-brain FDR or FWE with a reasonable cluster size 
threshold. You might consider thresholding at p < .1 or something if p < 
.05 is too restrictive; justifiable in my opinion, given how different 
searchlight data is from 'normal' fMRI data.

Given how few subjects you have, I'd also present the single-subject 
maps; obvious results in each subject makes the group results convincing 
even if the group-level p-values are less significant than you might hope.

good luck,

On 7/5/2012 12:21 PM, Mike E. Klein wrote:
> Hi everyone,
> I'm attempting to threshold group data for a searchlight-based MVPA . I
> am performing the group-wise stats via a standard top-level analysis in
> SPM (using single-subject searchlight accuracy maps as inputs). I am
> having difficulty figuring out where to set significance thresholds. SPM
> is using a purely random-effects calculation on the data (n=9, so df=8),
> leading to enormous t-thresholds (~16), which are impossible to reach
> and seem way too conservative. If I do small-volume corrections on our
> a-priori regions of interest, the effects are significant (but not by
> much...t-thresholds in the 8s), so this seems less than ideal (and
> ignores most of the brain).
> Typically, for GLM analyses, we use a "mixed effects" model, which
> incorporates both within- and between-subjects statistics, yielding an
> "effective" degree of freedom (which is much higher than the number of
> study participants, though much lower than the total number of trials in
> the experiment). However, I am not sure (a) how to calculate this for an
> MVPA study or (b) if the same set of assumptions hold. Our nine subjects
> each underwent 9 functional runs (used for 8 -> 1 leave one out cross
> validation). So each subjects searchlight map was reflecting an average
> of these nine folds. We used 81 total examples per condition (9 per
> run), which were temporally averaged, leaving 27 examples per condition
> that were fed into an SVM. Single-subject results were warped into
> standard space and also explicitly smoothed with a 7mm gaussian kernel,
> before being fed into SPM.
> We have strong results, so really I'm looking for the "most proper" way
> to perform searchlight group significance testing. Because we're doing
> 35,000-45,000 spheres per subject, I don't think permutation testing is
> feasible. There's also the option of reporting p<0.05 FWE stats for the
> pre-defined ROIs, and p<0.001 (uncorrected) for the rest of the brain,
> for completeness sake.
> Any advice is greatly appreciated!
> Best,
> Mike
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Joset A. Etzel, Ph.D.
Research Analyst
Cognitive Control & Psychopathology Lab
Washington University in St. Louis

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