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Hi Serena Basically, the registration takes about 5 to 10 minutes per comparison. The problem is that each subject is compared against each other so in your case that is 2116 comparisons. Multiply that by 5 and divide by the number of minutes in the day and you get 7.34 days. That is using single thread processing. I recently run the same with 180 subjects but split things up to optimise use on a 4 by 32 core to get through the 32400 comparisons :) Hope this helps Cheers Geoff From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of sere f Sent: Saturday, 4 October 2014 1:18 a.m. To: [log in to unmask] Subject: [FSL] problems with tbss_2_reg Dear FSL users, I have a problem with tbss_2_reg -n I have 46 subjects and I run the script 3 days ago and it is still running. Is it ok ? or is it tanking too much time? Thanks Serena