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Hi, Have a look at the easythresh tool, that might simplify things for you a bit. cluster will also do. However, when you look into the easythresh script, you will notice, besides the relevant options for a cluster based thresholding, that it also produces an estimate for the smoothness of the data (smoothest). I hope this helps, wolf On 03/21/2013 05:17 PM, Sean wrote: > I'm looking for a way to perform FSL's cluster thresholding from the command line. I'm hoping to do it the same way FEAT does it in post-stats, but I'll be running it on a single NII file that wasn't generated by FEAT. I've looked into the cluster command, but as far as I can tell this only reports statistics about clusters. Is this possible to do, and if so, how is it done? Are there any extra files (i.e., registration transformation matrix, etc) that I'll be needing? Thanks for your help.