Dear FS experts,

I ran cortical thickness analysis as previously explained in Wiki :

Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

1. My data is previously cached so I ran the command : mris_preproc --fsgd gender_age.fsgd  --cache-in thickness.fwhm10.fsaverage  --target fsaverage --hemi lh  --out lh.gender_age.thickness.10.mgh

2. GLM analysis: mri_glmfit  --y lh.gender_age.thickness.10.mgh  --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx  --surf fsaverage lh  --cortex  --glmdir lh.gender_age.glmdir

3. Correction for multiple comparison  mri_glmfit-sim  --glmdir lh.gender_age.glmdir  --cache 4 neg  --cwp  0.05  --2spaces

In order to do cluster-wise correction for multiple comparisons, I ran the command “mri_glmfit-sim” (step3). This command is calling, internally, the command “mri_surfcluster” as follow:

mdline mri_surfcluster --in lh//2G0C/sig.mgh --csd /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd --mask lh//mask.mgh --cwsig lh//2G0C/cache.th13.pos.sig.cluster.mgh --vwsig lh//2G0C/cache.th13.pos.sig.voxel.mgh --sum lh//2G0C/cache.th13.pos.sig.cluster.summary --ocn lh//2G0C/cache.th13.pos.sig.ocn.mgh --oannot lh//2G0C/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf lh//2G0C/cache.th13.pos.pdf.dat --cwpvalthresh 0.05 --o lh//2G0C/cache.th13.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white

Kindly, I have the following questions:

1. How the command mri_surfcluster choose the fwhm for the flag “csd” . In the previous command it shows fwhm=15.

2. What is purpose of using the flag Bonferroni in the previous command

3. If we are doing cluster wise correction, what is theexact usage of the flag “--vwsig”

Thanks for your patience !

Looking forward to learn from you

Mohamad