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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. < 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:

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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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Thanks for the help!

On Wed, Dec 4, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

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:

...

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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. <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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