I can't delete my message, but I solved the problem.
@SUMA_AlignToExperiment -exp_anat <afni_T1> -surf_anat <SUMA>/SurfVol -align_centers -wd -prefix <prefix> -surf_anat_followers <SUMA>/aseg.nii
I guess I needed the -align_centers and -wd combo with the orig surf anat and aseg to follow...
Edited 2 time(s). Last edit at 12/15/2014 10:38PM by dmoracze.