Hello,

I was wondering if I could get some help with the parameters for slow_surf_clustsim.py?

I'm doing a somewhat basic surface area analysis using values extracted from Freesurfer. After extracting surface area values for each subject/vertex morphed to fsaverage, I get a file I called lh.area.00.mgh. Then, I smooth it using mri_surf2surf and FWHM=10, which results in lh.area.10.mgh. I then extract the table to run my analysis in R/Python. I currently export the results to a 1D file and plot them in SUMA, and would like to set cluster-level correction there.

1) Does FWHM map 1:1 to blur? In other words, can I just use:

slow_surf_clustsim.py -save_script surf.sim \
-on_surface yes \
-uvar blur 10 \
-uvar spec_file ${SUBJECTS_DIR}/fsaverage/SUMA/fsaverage_lh.spec \
-uvar surf_vol ${SUBJECTS_DIR}/fsaverage/SUMA/T1.nii

2) I'm a bit confused about when to use vol_mask. Is it the case that for thickness or volume analysis it would be needed, but if it's surface area it's not (and only -on_surface yes is used)?

3) Does the hemisphere I used in .spec matter? I normally visualize the results using fsaverage_both.spec, but that broke slow_surf_clustsim because it found multiple matches for smoothwm.

4) Now, say I use a completely different surface. For example, an amygdala surface extracted using MAGeT (https://github.com/CobraLab/MAGeTbrain). I'd like to do the exact same cluster correction there. Is it as simple as providing my anatomical template, spec, and -uvar vol_mask to mark only the amygdala?

Thanks in advance,

Gustavo