The preprocessing by AFNI proc is now ready and the alignment results look good. Regarding alignment, I used the raw functional scans as suggested by you and the following options:

-align_opts_aea -cost lpc+zz -giant_move \
-align_unifize_epi local \

Two more question came up.

Question 1:
When checking the "MNI152 2009 template SSW.nii.gz" underlay vs. "full_mask.subject..." overlay, I see that the EPI functional mask does not perfectly match the MNI152 template. I assume that the result is still good enough, because the underlay is the original MNI152 brain, and not the aligned anatomical brain by the respective subject. Hence, this overlap cannot be perfect anyway. Is that correct?

The first attached image shows what I am talking about, and MNI152 template vs. full_mask comparison looks more or less the same as the one shown here for all subjects.


Question 2:
Three of twenty subjects gave me "EPI variance lines warnings" in the QC index by AFNI proc. I wonder if that is related to the fact that I manually set the TR before preprocessing the data with AFNI proc, or if that problem is related to something else? I attached a second image for this problem.