Howdy-

It looks like your anat has already been skullstripped; so you should include the following in either/both afni_proc.py and align_epi_anat.py:

-anat_has_skull no

If there is a large rotational difference between the EPI and anat to start with, then going above and beyond -giant_move might be necessary-- try "-ginormous_move" instead (yes, it's the option's real name...). I can't tell if there might be large relative rotation in the attached images, but perhaps try this.

Given the inhomogeneity of the EPI, it might be possible that too much is being stripped away by the auto-masking (done with 3dSkullStrip by default). You could try including:

-epi_strip None

Re. cost functions:
The T1w anat has tissues in order of decreasing brightness: WM, GM, CSF. The EPI looks pretty inhomogeneous. Can you see the ventricles in it clearly? If the pattern of tissue brightness looks more like normal EPI (which is mainly inverted relative to the T1w volume), then using just the "lpc+ZZ" cost function should be your best bet-- the "+ZZ" part adds some stabilizing alignments. But if the inhomogeneity or other EPI features makes the tissue contrast of the EPI look different than normal, "lpa+ZZ" cooould have better alignment.


Separate note on skullstripping and (nonlinear) alignment to standard space: using @SSwarper to accomplish both skullstripping and warping is quite recommended; the results can be fed into afni_proc.py (see the help of that program for the recipe for doing so). It generally gives nice nonlinear alignment to standard space, as well as a well-skullstripped anatomical.

--pt