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
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