Hello AFNI experts,
As much as I dread asking for help in public, this issue has me stumped. I'm trying to follow afni_proc.py example 11 to pre-process some resting state data. Following that example, I first ran @SSwarper to calculate the transform of the anatomy to MNI space. Then I provided those images to afni_proc.py, along with -align_opts_aea that I separately verified to properly align the anatomy to the EPI images. Running the script afni_proc.py creates does indeed properly align the anatomy to the EPI, as verified by overlaying pb02.subjnum.r01.tshift+orig onto anat_al_junk+orig. However, when I check for alignment of the EPI to MNI space, it's clearly off (shown by using anatQQ.subjnum+tlrc as the underlay and pb03.subjnum.r01.volreg+tlrc as the overlay). I'll paste the actual afni_proc.py command next. And of course I'd appreciate any direction you can give me on this!

@SSwarper -input anat.nii \
-subid $subj \
-odir anat_warped \
-base /usr/lib/afni/bin/MNI152_2009_template_SSW.nii.gz

Then:
afni_proc.py \
-subj_id $subj \
-dsets rest+orig \
-blocks despike tshift align tlrc volreg blur mask scale regress \
-copy_anat ./anat.nii \
-anat_has_skull yes \
-anat_follower anat_w_skull anat FT_SurfVol.nii \
-anat_follower_ROI aaseg anat aparc.a2009s+aseg.nii \
-anat_follower_ROI aeseg epi aparc.a2009s+aseg.nii \
-anat_follower_ROI FSvent epi FT_vent.nii \
-anat_follower_ROI FSWe epi FT_WM.nii \
-anat_follower_erode FSvent FSWe \
-tcat_remove_first_trs 2 \
-align_opts_aea -epi_strip 3dSkullStrip -skullstrip_opts -blur_fwhm 2 -push_to_edge -cost lpc+ -giant_move -check_flip \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets anatQQ.$subj.nii anatQQ.$subj.aff12.1D anatQQ.${subj}_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 4 \
-mask_epi_anat yes \
-regress_censor_outliers 0.1 \
-regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts \
-scr_overwrite \
-html_review_style pythonic

Incidentally, the QC webpage output doesn't seem to show any outlines that are useful for checking registration. Not sure if that's obtained a different way or what.