Hello,

Thanks for posting the script. Any chance of posting the alignment photos on google as well?

It appears that you used a pretty old version of afni_proc.py to generate the script (2014), so I would first suggest updating your version of AFNI. For the alignment, I suspect that adding "-giant_move" to your align_epi_anat step would fix the issue or in the original afni_proc command that generated the tcsh script to add

-align_opts_aea -cost lpc+ZZ -giant_move

If you suspect a skull stripping issue, then you can use the "new" (circa 2017) @SSwarper to perform the skull strip and also registration to standard space. Pair that with Example 6b here and go from there.

If you post the afni_proc commands you write we can help tailor it further. But example 6b should be a good start point for your analysis given the event-related design and options that appear to be used before.