Hi, Misho-

OK, I think your version of AFNI is fairly old---what is "afni -ver"? I guess this because your ve2a block has the anatomical as underlay with edges of the EPI as overlay (that has been reversed in APQC presentation for a while), and there is no vorig block there.

You can update AFNI with:

@update.afni.binaries -d

Thanks for sending the raw EPI images, though, anyways. A couple things to note:
+ The tissue contrast looks odd: typically, in an EPI, I am used to seeing bright ventricle, fairly bright GM, and WM is the darkest. See the attached image (from the Bootcamp example EPI in AFNI_data6/FT_analysis, actually--the APQC image of vorig). In your case, the ventricels are dark, but the GM is relatively bright. What kind of EPI contrast is this? This will probably change the appropriate cost function that should be used---lpc is for when the source and base dsets have opposite contrast; here, it isn't really a full inverse tissue contrast, but it also isn't the same contrast as the T1w anatomical (because the GM and WM contrast is opposite). I wonder about trying "nmi"?
+ There is a fair amount of distortion in the EPI: see the frontal regions, and medial regions just superior to the sinuses. That will also affect alignment. The frontal distortion looks like B0 inhomogeneity distortion. That will kind of limit the amount of alignment that the affine registration can do; but I don't think there is enough detail to try anything nonlinear (there typically isn't with EPI dsets).
+ I don't think -giant_move will do anything here---as you say, the initial overlay is pretty good. I think the biggest issue is finding a good cost function to deal with this EPI tissue contrast.

Re. changing the proc script: that can be OK if you really have to, but that often isn't ideal, esp. for being able to re-run or tweak re-runs easily. It might be worth checking with Rick if there are ways to accomplish your goals with afni_proc.py options directly. Esp. since you appear to have an older AFNI version, perhaps some updates since then will help.

--pt