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?

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?

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> 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