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Thank you so much for your input, it was very helpful and I really appreciate it.
Regarding your question with relation to my 4th question, when I run the below command line to visualize my results after correcting for multiple comparisons using monte-carlo at 1.3 significance level in this example, I assumed the clusters that appear on freeview are only my significant clusters (clusters that survived monte carlo correction) since I put " cache.th13.abs.sig.cluster.mgh" and then as overlay " cache.th13.abs.sig.ocn.annot " in my command line. If not, will you please tell me how I can see only clusters that are significant after correction for multiple comparisons (at 1.3 sig level in this case)?
Also, in my command line, I can put either lh.pial or lh.inflated to see the results//clusters on the pial or inflated surface, respectively. Correct?
vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 3d
Thank you so much,
Avi