Hi-

Thanks for posting that.

OK, I would update the align_opts_aea option (for controling anatomical-EPI alignment, AEA) to be:

-align_opts_aea           -cost lpc+zz -giant_move -check_flip     \

That is our general starting point---from the options you cited above, the "-giant_move" might be necessary to open up the parameter search space for the alignment. The "-check_flip" is generally useful as a quick check against left-right flip badness, which happens:
https://www.frontiersin.org/articles/10.3389/fninf.2020.00018/full
You can also keep the "-Allineate_opts -source_automask+4" part, too (though I am not sure it is necessary in the updated case---I think the -giant_move might have that as part of it). I also realize I am not sure what previous iterations you might have had of the command overall...

I would also add this new option:

-align_unifize_epi local

... which often helps overcome EPI brightness inhomogeneity.

I would add this for letting the program pick the EPI volume with minimal numbers of outliers to be the EPI-anatomical reference volume, as well as "motion correction" reference volume:

-volreg_align_to          MIN_OUTLIER                              \

That is the most secure way to go for those processes.

You should state whether the anatomical has a skull on or not, so the program knows:

-anat_has_skull           no                                       \

(adjust "no"/"yes", as necessary). In my comment below about using @SSwarper before afni_proc.py, you would be able use a skullstripped output from that former program and then put "no", as here.

I see you have: "-regress_anaticor". To do anaticor, I would typically suggest running FreeSurfer first to get higher specificity segmentations of tissue for defining where to get the tissue-based signals from.

For nonlinear alignment, we would generally recommend running @SSwarper first, and then passing the results into afni_proc.py to be used. How does that sound? It combines the nonlinear alignment with anatomical skullstripping, as a bonus.

I would add in this option for some more QC items:

-radial_correlate_blocks  tcat volreg                              \
     -volreg_compute_tsnr      yes                                      \

You might only have one EPI run, but I generally include this option, include this option, so I don't forget to in cases that I have more than one:

-regress_motion_per_run                                            \

--pt