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
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