Hi, Gabor.

I've already done fslreorient2std and yet the problem ensued.

I've just written an email with the input and output images for each step of commands I've performed. Any comments on it will also be a lot of help.

Your advice is deeply appreciated. Thanks!

Sincerely, Sooyun Cho.

보낸사람 : Gabor Perlaki <[log in to unmask]>
받는사람 : <[log in to unmask]>
받은날짜 : 2016-11-28 (월) 18:42:27
제목 : Re: [FSL] "run_first_all" not working for children (ages 11~13)

As far as I know no BET will be applied at all during run_first_all, so I really don't understand your problem with BET.

"As I've said in my previous mail, I'd already tried using the non brain extracted T1 images for run_first_all, but a same error regarding non-brain tissue removal (assuming either for either BET or FLIRT) seemed to occur for a couple of my subjects' images."

As Niels suggested, if your images are not axial you should run fslreorient2std before run_first_all.

Best,
Gabor