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 <owensma...@gmail.com > <mailto: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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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