Firstly, yes. I was making that error, and many thanks for catching it!

Unfortunately, even after applying that fix, the problem remains, but it does explain why some of my earlier attempts to figure things out on my own failed. I will try to duplicate a simpler model and see if that works.

Follow up question.

If I have a 2-level factor that I want to include as a nuisance variable, (e.g. gender), would I be able to define that as a numeric variable with values 0 and 1, rather than splitting up my other categories?

Thank you for your help,

-Eric

On Thu, Aug 13, 2020 at 9:42 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Do you have a 1-off error? Ie, FS starts counting at 0 and matlab starts counting at 1. So vertex 53263 is vertex 53264 in matlab.

On 8/12/2020 5:31 PM, Eric Cunningham wrote:
External Email - Use Caution

Hello Freesurfer Experts,

I am trying to plot the ${meas} values at the maximum vertex in a significant cluster found by the group analysis pipeline (mri_glmfit).

I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh. I read this file into matlab using MRIread. (mgh=MRIread(${path}/rh.cbd7.area.10.mgh);) After running mri_glmfit and mri_glmfit-sim, I found a significant cluster with maximum at vertex 53263. I read the values at this vertex using matlab again (values=mgh.vol(1,53263,1,:)). I then tried to duplicate the p value that mri_glmfit gave me at that vertex in R, and was unsuccessful (the p values did not match, and were actually quite different).

I had assumed that mri_glmfit ran a glm at every vertex of the smoothed mgh file created by mris_preproc, and that the p values of that glm were assembled into sig.mgh. Was this assumption wrong?

Thanks,

-Eric
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