Hi Jennifer,
What is the exact pair of SUMA and AFNI commands you ran that led to the bad alignment?
If you used for -sv the volume that you passed to FreeSurfer, rather than the one created in the SUMA/ directory by @SUMA_Make_Spec_FS then you may very well get a bad alignment.
Also, assuming you are using a recent version of AFNI/SUMA, I recommend you start using @SUMA_Make_Spec_FS with the option -GIFTI.
Let me know which volume you used for the -sv option and we'll take it from there.
cheers,
Ziad
