Re: [Freesurfer] Issue with extracted thickness value from significant cluster or peak vertex
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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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Issue with extracted thickness value from significant cluster or peak vertex
External Email - Use Caution 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Issue with extracted thickness value from significant cluster or peak vertex
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? 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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
