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Hi,

The simplest thing is to break down your ANOVA into the t-tests of interest and run those.  For example, if you want to compare stim1 to stim2, you would run a level 2 (fixed effects) analysis to calculate the paired difference (subject-specific models) and then run a 1-sample t-test on this in a group model.  This simplifies the repeated measures aspect of the data.  

Hope that helps,
Jeanette

On Thu, Sep 27, 2012 at 3:44 PM, Cara Damiano <[log in to unmask]> wrote:
We are interested in doing a group (control, patient) x stimulus type (4 levels) ANOVA in FSL but are not sure how to do this. We have tried to set up F tests for the within-subjects factor of stimulus type and then feed these fstats to higher-level analyses but this doesn't seem to work. Any suggestions? Thanks!

Cara