Hi, I have been following the documentation for mri_glmfit-sim and need a bit of clarification. The point where we run tksurfer with the -annot option, it seems that it displays all the clusters (regardess of the significance) on the average brain. When I run it, it looks like cortical parcellations are being displayed on the brain. It also displays the clusters (within the parcellations); so it seems to be working. I am just curious as to why the parcellations are being displayed. Here is the command I am using.
*tksurfer fsaverage rh inflated -annot mc-z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray*
But more importantly, I would like to know how to interpret what I am seeing correctly. I understand that the p-value threshold can be set by -fthresh (2 corresponds to p value of 0.01). In the cluster summary (it found 25 clusters), I am seeing CWP of 0.001 for 24 of the 25 clusters. What does this significance mean as calculated by the command? Is this corrected across the whole brain?
Thank you, Devdutta