Hi all,
I'm trying to run Monte Carlo simulations on cortical thickness data I got using mri_glmfit, but I'm running into some errors.
1) I used the command
mri_glmfit-sim --glmdir lh.thickness.fwhm20.diagnosis_scanner.dods.glmdir/ --cache 2.0 pos
The error I receive says "cannot find /usr/local/freesurfer_x86_64-5.1.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm40/pos/th20/mc-z.csd"
I'm wondering why the script is looking in the directory "fwhm40" when the data is smoothed using FWHM 20. The directories available under fsaverage/lh/cortex go from fwhm01 to fwhm30.
2) Also, for another test I'm running, I created my own average subjects (instead of using fsaverage). Is there a way to generate the files that are created under /average/mult-comp-cor for this average subject so that I don't have to use the "--sim" flag to run simulations?
Thanks, GT