On 1/9/19 10:35 AM, Max Owens wrote:
>
>         External Email - Use Caution
>
> Hi,
>
> I just wanted to follow up and see if there was anyone who could
> answer my questions:
>
> 1.What is the unit of effect size for the gamma.mgh file created by
> vertexwise GLM Analysis using mri_glmfit?
Same units as the input (ie, --y)
>
> 2.Based on two previous posts
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52144.html and
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57316.html)
> I tried to calculate Cohen’s d in all significant clusters resulting
> from clusterwise multiple comparison correction of a vertexwise GLM
> using mri_glmfit. I did this by dividing the gamma.mgh file by
> rstd.mgh to create a cohensd.mgh file (fscalc gamma.mgh div
> ../rstd.mgh -o cohensd.mgh). Then from the output of that operation I
> extracted the mean value in each significant cluster from my
> vertexwise analysis using mri_segstats (mri_segstats --i cohensd.mgh
> --seg cluster.sig.ocn.mgh --exclude 0 --o sum.dat). My understanding
> was that this would yield the average Cohen’s d of each cluster.
> However, if it is indeed Cohen’s d the effect sizes yielded (between
> .01 and .02) are so small that they should be undetectable given my
> sample size (N=1104). This leads me to believe that the outputs are
> not in fact the average Cohen’s d of the cluster. Can anyone provide
> any clarification of what the output file of this process means?
> Specifically, what is the unit of effect size?
Cohen's D  is defined for a two group analysis as
(mean1-mean2)/PooledStdDev. Do you have a two-group design? If not, then
Cohen's D might not be the right effect size to use.
>
> Please let me know if I can clarify anything.
>
> Thanks,
>
> Max
>
> On Fri, Dec 7, 2018 at 1:02 PM Max Owens <owensmax03@gmail.com
> <mailto:owensmax03@gmail.com>> wrote:
>
>     Hi Freesurfer Experts,
>
>     I have two related questions about the measures of effect size
>     that can be derived from a vertexwise GLM analyses conducted in
>     Freesurfer:
>
>     1.What is the unit of effect size for the gamma.mgh file created
>     by vertexwise GLM Analysis using mri_glmfit?
>
>     2.Based on two previous posts
>     (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52144.html
>     and
>     https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57316.html)
>     I tried to calculate Cohen’s d in all significant clusters
>     resulting from clusterwise multiple comparison correction of a
>     vertexwise GLM using mri_glmfit. I did this by dividing the
>     gamma.mgh file by rstd.mgh to create a cohensd.mgh file (fscalc
>     gamma.mgh div ../rstd.mgh -o cohensd.mgh). Then from the output of
>     that operation I extracted the mean value in each significant
>     cluster from my vertexwise analysis using mri_segstats
>     (mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude
>     0 --o sum.dat). My understanding was that this would yield the
>     average Cohen’s d of each cluster. However, if it is indeed
>     Cohen’s d the effect sizes yielded (between .01 and .02) are so
>     small that they should be undetectable given my sample size
>     (N=1104). This leads me to believe that the outputs are not in
>     fact the average Cohen’s d of the cluster. Can anyone provide any
>     clarification of what the output file of this process means?
>     Specifically, what is the unit of effect size?
>
>     Thanks in advance for your help!
>
>     Max
>
>
>
> --
>
> Max M Owens
>
> Postdoctoral Fellow
>
> NERVE Laboratory
>
> University of Vermont
>
>
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