Yes, but threshold it first, eg
mri_binarize --abs --i sig.cluster.mgh --min .000001 --o newmask.mgh

On 12/4/19 1:38 PM, cody samth wrote:
>
>         External Email - Use Caution
>
> 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.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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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