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Here's the pathway I took.  I'm unsure if this is ok, considering the way FSL thresholds results.

1.  3 Groups:  Schizophrenia, Schizophrenia Relatives, Controls

2.  Contrast is Red Cue vs. Green Cue (RCvsGC)

3.  Group level analysis:  Controls (1) > Relatives (-.5) > Schizophrenia (-.5)

4.  Results in RCvsGC in Controls > Relatives > Schizophrenia with cluster threshold of 2.3.

5.  Use fslmaths to intersect the cluster_threshold_mask_stat with inferior frontal gyrus (Harvard Oxford) and create mask.

6.  Run uncorrected main effect of RCvsGC in each of 3 groups.

7.  Use featquery to mask the uncorrected main effect of RCvsGC in each group with the mask created in step 5.

8.  Extract mean time series (which I understand is each subject mean %change in activation when you click on mean time series in featquery results)

9.  Compare the 3 groups using t.tests, anova, etc.... to establish non-overlapping error bars (or lack there of).

My main question would be in relation to using that specific interaction(RCvsGC) and contrast(1, -.5, -.5) to create a mask.  Is this principled.  Secondly can I use that mask to pull beta weights associated with uncorrected main effects, because the group level was already cluster thresholded?

Edward H. Patzelt
University of Minnesota