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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