Hi, Zhang-Lei-

I'm a bit curious what your version number of AFNI is? I wonder if it is a bit old? You can check by running "afni -ver".

Because of the order of your blocks, the volreg results are shown in the final space (and this is basically what we recommend in most cases, so that is the correct thing to do). But I suspect that the EPI->anatomical alignment might not be good, so the final placement of the EPIs is off. (It is possible the anatomical->template alignment is bad, as well-- that should be checked.)

Do you see a directory in your afni_proc.py results directory called QC*/? That contains an HTML that you can open (QC*/index.html) to view a lot of quality control automatically created by afni_proc.py. That would show you individual alignments to check. A lot of its features are described here:
[afni.nimh.nih.gov]
... and we recommend that you have Python+Matplotlib installed on your computer, and then you can use the "-html_review_style pythonic" for an even nicer style of the QC HTML.

There are also a script for single subject (ss) review, called @ss_review_driver, that helps guide you through viewing things in the GUIs, esp. alignment. (Many of these features have been integrated into the QC HTML, as well.)

Does that show any alignment issues between EPI->anatomical or anatomical-> template?

--pt