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Hello Freesurfers,
I am using mri_glmfit-sim to find significant clusters using permutation simulation. My command is as follows:
mri_glmfit-sim \ --glmdir lh.cn_ad.glmdir \ --perm 1000 3.0 pos \ --cwp 0.05 \ --2spaces \ --bg 1
When I opened the *.sig.masked.mgh, I noticed that some vertices below the cluster forming threshold (3.0) were also included (the lowest value I found in the cluster was around 2.5). These vertices also seem to be on the edge of the cluster. Based on the FsTutorial, the permutation simulation should exclude all vertices below the cluster forming threshold. Is there any sort of smoothing done on the clusters that could have caused the vertices below CFT to be included?
I checked the mail archive and found this thread that have exactly the same question, but with no answer: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html
Thank you, Fengdan