On 10/22/2020 3:58 AM, Julian Macoveanu wrote:
> External Email - Use Caution
>
> 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?
No
>
> 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?
Probably your SPSS model is different. About once a year someone writes
to the list to report this effect, but I never hear back when I ask them
to confirm that the model is exactly the same. One thing you can easily
try is to do the analysis in matlab using our tools, eg,
y = load('y.ocn.dat');
X = load('Xg.dat');
C = load('contrast/C.dat');
[beta rvar] = fast_glmfit(y,X);
[F p] = fast_fratio(beta,X,rvar,C);
p will be a vector of p-values, one for each cluster
>
> 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 group 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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