Hi pt,
I think that alignment was not performed properly. I am doing it again with FSL but at the same time trying to use AFNI's @SSwarper because it looks more convenient. But when I try to call it, I get this error:
I tried adding the AFNI directory to my path like in this suggestion but it does not help. Do you know what might be going wrong?
I thought it might be because I am running a version of AFNI from 2021, but when I look into the AFNI directory, the script for @SSwarper is there. Do you know what this error might mean?
Also I can make a separate thread if that would be better since this is completely different from the original issue haha