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Thanks for your help. Again the original message was "Correct Perm has max t 0 & rank 200 out of 200 completed permutations". Thomas Nichols wrote: > It's hard to tell what could be causing this; my first guess would > be image data problem. Did an equivalent parametric analysis run OK? Actually I don't know how to do a parametric analysis with one scan per subject. > You might try > > load SnPM_cfg > load SnPM > if (~bhPerms); MaxT=MaxT(:,1); end > hist(MaxT(:),40) > > This will give you a plot of the permutation distribution. If it's just a > bar at 0, then it would seem that you have all-zero data. Let me know > what it looks like otherwise. 1) The histogram shows some permutations with value 0 but the distribution is spread out across a range of MaxT values (0 to 0.74), not clustered at 0. 2) I can imagine that (since we're not doing a paired comparison) this group comparison may have mostly negatives and no signif. positives, which may explain part of these results. 3) When I run spm_snpm_pp with positives, even at a p=0.99 threshold, I get no signif. pixels. But when I run it with negatives, I get a big list of pixels with the max t value being 3.09. Shouldn't this be counted in determining where in the list of scans this comparison falls (i.e., shouldn't max(|t|) be the omnibus statistic used rather than max(t))? How do I tell where t=-3.09 falls in the list of 200 scans? Can I generate a histogram for max(|t|) or at least max(-t)? Thanks a bunch, Kevin Black