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Dr. Greve,
Thank you for this information. The input to mri_glmfit was an mgh file of structural MRI data from several subjects warped into a common space and concatenated. What would that make the units of the input (--y) file and the output gamma file?
To the second question, the analysis is continuous (association of several continuous cognitive variables and area/thickness/volume) so I am thinking perhaps the output file being produced by this operation is not Cohen's d. Is this possible or does that operation always produce Cohen's d? I found a line on the documentation that says - "For measuring the contrast to noise ratio (CNR) in mri_glmfit, the file cnr.nii is generated by the contrast value (gamma) divided by the residual stddev (rstd)." Does that make my output file a contrast to noise ratio?
Max
On Thu, Jan 10, 2019 at 11:40 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
On 1/9/19 10:35 AM, Max Owens wrote:
External Email - Use CautionHi,
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
andhttps://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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