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Thanks, for your input. It's interesting that there isn't a more standard
way of approaching it. If i wanted to constrain my post-hoc to be within
the cluster(s) from the main effect how would I go about running this
through mri_glmfit? Would I include the --mask sig.cluster.mgh in the
command for mri_glmfit and then aslo mri_glmfit-sim?

On Mon, Dec 2, 2019 at 6:40 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I don't think there is a standard way to do this. A vertex-wise analysis
> is not the same thing as a averaging over a group of vertices. I guess you
> could constrain your post-hoc analysis to be within the main effect
> cluster; that would be most consistent. But I don't think you'd have any
> problems getting it published either way.
> On 12/2/2019 3:12 PM, cody samth wrote:
>         External Email - Use Caution
> Hi,
> I have a statistical question about how to approach reporting results from
> FreeSurfer analyses containing three groups. I ran a group effect (F-test)
> and then post-hoc tests looking at pair-wise comparisons between the three
> groups. My question is why is that we run separate vertex-wise analyses for
> the post-hocs rather than extracting the values from significant clusters
> and running post-hocs in a statistical software for just the regions where
> a significance difference was found (ie the clusters)? As a post-hoc vertex
> wide analysis can lead to different results.
> For example in my group effect contrasts I found a cluster in the parietal
> lobe. Whereas in my post hoc-vertex wide analyses one of them found two
> clusters 1) within the parietal 2) within the frontal lobe. If I choose to
> run these post-hoc analyses via freesurfer (ie vertex-wise) rather than
> extracting the results to analyze in a statistical program, is it standard
> to report the second cluster? Even though it didn't come up in the group
> model? If so is there a paper that people reference that uses this approach?
> Thanks,
> Cody
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