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Can you post the code you used? Have you tried running 'randomise_parallel' just once, without looping or using your wrapper? ________________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Isaia Panduri [[log in to unmask]] Sent: Friday, January 16, 2015 4:06 AM To: [log in to unmask] Subject: [FSL] ransomise_parallel does not output all contrasts Hi everybody! I'm running vertex analysis on a rather big sample (>900), and I'm using randomise_parallel in order to test statistical significance. My problem is that randomise only output one out of two contrasts that are present in the .con file. The script does recognize that there are two contrasts in the file, as it echos "Generating 100 fragments for 2 contrasts with 100 permutations per fragment", it run smoothly till the end without any error, and it pass to the following structure in the for loop. However, when I look in the output directory, I find two t-stat files, but the _p_ and _corrp_ images for the first contrast only. The strange thing is that this happen only for certain structures in the same loop, so that for some structures this problem is present while for other structures I have the whole set of images. Have you got any hints about what's happening ? I created a function randomise_wrapper to simply loop on several structures and several matrices, and I'm running parallel version of this function on several different terminal. Can this be an issue ? Thank in advance!