My recommendation is to reprocessing using Subject_SurfVol.nii as your "anat" dataset in afni_proc.py with the -anat_has_skull set to "no". Then make sure that you have things aligning to the anatomical via -volreg_align_e2a. I've found this is generally the safest and also benefits from all of the AFNI automated QC images.
As an alternative, you can use
@SUMA_AlignToExperiment and specify your follower datasets to include your aparc and aseg datasets.
Also if you're not already doing so, we generally recommend using the -NIFTI flag in your
@SUMA_Make_Spec_FS commands.
