Dear Freesurfer experts:
I ran into a confusing problem when applying Monte Carlo simulation to control for multiple comparisons. I am using the buckner data from tutorial dataset.
I first tried the simulation based on Freesurfer;s 2012 manual: (http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-2...)
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite
This produced a "mc-z.negative.sig.cluster.summary". In this text, no clusters survived correction.
Later on, I applied on a slightly different script, based on Freesurfer tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwis...)
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces
It produced a "cache.th40.neg.sig.cluster.summary" this time. But according to this result, 22 clusters survived.
Now I am quite confused, because both corrections have the same voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the drastic discrepancies come from and which result is more reliable?
Many thinks in advance.
Best,
Karl