Howdy-

Oh my, that did go horribly wrong...

I am noticing your reference volume is the MNI average; that is pretty blurry, without a lot of detail to align well with nonlinear alignment. We typically recommend using another MNI volume with more detail, such as the MNI 2009c volume, and esp. using the MNI*SSW*nii.gz volume (for performing nonlinear alignment using @SSwarper prior to running afni_proc.py, and then using the alignment results as inputs to afni_proc.py). See the attached image-- the top is the MNI*SSW* volume, and the bottom one is the MNI average. You can see the difference in level of detail...

We can discuss this more, but I'll point out some useful background for these considerations:
1) Some description of templates (and atlases), including how to pick them:
[www.youtube.com]
2) Also, the alignment series would probably be really useful to watch:
[www.youtube.com]
There are maaany considerations that come into alignment.

--pt