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Sorry I had to re-posted this since since it quickly moved down the
list without an answer

Julian Macoveanu Thu, 22 Oct 2020 00:59:50 -0700

Hi,
I am using FS 7.1.0. After running the surface thickness GLM analysis
I get one cluster after correction for multiple comparison showing a
significant group difference. I want to make a plot illustrating this
group difference. However, when using the mean values from:

cache.th30.abs.y.ocn.dat, I don’t see the expected group difference in
these values.

Question 1)
Are the subjects cluster mean values in y.ocn.dat adjusted for the
covariates I used in the fsgd file? E.g. age, sex and TIV?

Question 2)
I inserted these mean cluster values from y.ocn.dat in SPSS and tried
verify the statistics both with and without adjustment for covariates
and did not get the expected significant group region which I expected
in either case. Why is this?

Question 3)
I moved on to extract the thickness values from peak vertex in my
significant cluster. For this I used mris_convert which I just wanted
to be confirmed that is correct:

mris_convert -c lh.thickness.fwhm15.fsaverage.mgh
$freesurferdir/fsaverage/surf/lh.orig  output.asc

After extracting the thickness value for all subjects from the peak
vertex as reported by the sig.cluster.summary, I still have the same
issue as before, I find no expected group difference.

Interestingly, the significant cluster I found is part of the
superior_frontal region in aparc2009. When I extract these values it
almost shows significant group differences in the entire region, in
line with the surface GLM findings.

Thanks,
Julian

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