Dear FS experts, I ran cortical thickness analysis as previously explained in Wiki :
Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
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 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 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. Is this depends on how much I am smoothing in the previous steps?
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