Dear Freesurfer Experts:
I repost a question I have when applying Monte Carlo simulation to control for multiple comparisons. Your help is much appreciated.
I did the correction via QDEC GUI. In the section of Monte Carlo Null-Z
simulation, I set Threshold: 2.0 (0.01) and Sign: neg. This generates a
"mc-z.neg.th20.sig.cluster.summary"
file in each contrast folder.
Later, I use the in-line: command mri_glmfit-sim instead. My input is:
ri_glmfit-sim --glmdir Untitled --cwpvalthresh .05 --cache 2 neg --2spaces. This generates a "cache.th20.neg.sig.cluster.summary" file for each contrast.
My question is : are these two summary files the same, one from QDEC
GUI with name " mc-z..." and the other from in-line command with name "cache..."?
My next question is: In QDEC GUI, when the simulation is finished,
the GUI automatically illustrates the clusters/brain, based on a file named
"mc-z.neg.th20.sig.cluster.mgh". But I doubted if this is
post-correction results. What is the right way to view results after
correction?
Thank you very much.
Karl