Hi, Clément-
Sorry, that doesn't clarify things for me; I'm also not sure what viewer the images you are showing is using, so I don't know if it is doing something funny. Actually, in the images you sent, are you happy or sad with the alignment (and is that at the start or end of processing)? And I don't know what "transform" you have applied; the 3dinfo output looks identical for the rest dset, and I don't know what it is for the anat dset "afterwards". I don't know how afni_proc.py is "failing" for these dsets, either.
Sooo, could you please enumerate/clarify the steps.
--pt
