Hi Paul,
thanks for your comments and interest. Just a few rapid reply to your questions:
0) I am using TORTOISE_V3.1.1/DIFFPREPV311
1) I am using fat_proc_imit2w_from_t1w Ver. 2.2 (PA Taylor, Mar 1, 2018) and I don't see an output mask, I see a a skull-stripped version of PREFIX_t1w.nii.gz: you mean that I can generate a mask from this skull-stripped and use it?
2) why you sed "a warped version to standard space" I have just axialized to a reference (6DOF) not warped... isn't it?
To reply to other comments I have to check (and study more).
Cheers,
Giuseppe