We are doing a PPI analysis to look at amygdala connectivity with phase of task (preconditioning runs vs. generalization runs) and task stimulus (event) shown. I did the first level PPI on each of our runs with amygdala seed and task stimuli. I am having trouble figuring out where the task phase fits into this analysis. We want to look at differences in preconditioning which is runs 1 through 3 versus generalization which is runs 6 through 9. I know in SPM it can be done as a full factorial model with both phase and stimulus as factors, but I am not sure if/how it can be implemented in FSL. My only thought was to do the 2nd level twice, as a separate average on runs 1-3 and then runs 6-9, and then contrast those at the 3rd level. Any guidance would be much appreciated.
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