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Dear Diederick, We don't normally specify the size as a threshold, but rather use the FWE corrected probability. It is related to size though, and so if you have the size values (and they are validly calculated) then you can do it that way around. In that case you would use the --osize option (which puts a value into each voxel in a cluster that is equal to the cluster's size) and then use fslmaths with the -thr set to your cluster size threshold. All the best, Mark On 6 Jun 2012, at 20:41, Diederick Stoffers wrote: > Hi all, > > I have a collection of Z-maps and a table with cluster sizes needed to survive FWE-correction at different combinations of uncorrected and corrected thresholds. To my surprise it seems there is no easy way to output masks for a set cluster size threshold; the only I see is to combine the output from the cluster command, awk and fslmaths to get these masks. Am I correct or is there an easier way? > > Cheers, > > Diederick