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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 <owensma...@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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