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Dear Nils, thank you for your reply, which I happened to see just now. Just to make sure, I understood correctly: You are suggesting I use the -nan on my filtered_func_data , right? I just tested this, then using randomise with only 50 permutations to save time and then running cluter, but I still get the 'nans' in the columns. I did not create my files with any other program, though, so I am wondering where things went wrong. Still, since I inputed the corrected images (randomise outputs) to 'cluster' and then set my t to 0.95, should the numbers in the p and log(p) column, not just be 0.05 and log(0,05), respectively, since I define that in the very same command? Thanks a lot, Hannah