Hi, Joy-

Thanks for posting the output. Indeed, alignment *always* requires visual checking; note that we have the automatic HTML output to help facilitate this process of checking, too; from your afni_proc.py results directory,

afni_open -b QC_*/index.html

should open the APQC (afni_proc.py quality control) HTML; if you have python+matplotlib installed on your computer, you can add "-html_review_style pythonic" to your afni_proc.py command, and get the prettiest/most informative version of QC.

... Now, to address your actual question:
+ could you please post the output of "afni -ver"
+ could you please post your afni_proc.py command, and
+ could you provide an image overlaying any of the EPI volumes on the anatomical *before* alignment (i.e., the raw volumes)?
The third part will help us see how "far apart" the volumes are to start, which is typically the root of alignment evils. The second part will help us see any options you have provided about alignment already. And the first part will help us make sure we're all using a similar/modern AFNI version.


--pt