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Hi, That doesn’t look right indeed. Are these three the only subjects that you ran FIRST on, or did it run successfully for other subjects? And could you provide some more information on what version of FSL you are using and on what platform you are running it? I am not sure at this point what is causing this, but that might help narrow things down a bit. Thanks, Eelke > On 20 Nov 2015, at 18:09, SUBSCRIBE FSL lijen <[log in to unmask]> wrote: > > Hello, expert > I used run_first_all to segment but the result had three problems. > > The fist one, the blue(maybe brainstem) area is wrong! > The second, to run " run_first_al" but no show result file. > The last, the terminal show error messages. > I attach three attachments of my result picture. > > thanks, > Li_Jen > <F1.jpg><F2.jpg><F3.jpg>