Thanks, Taylor!
It did not throw any error after removing the tlrc-related commands. But it ended with "** surf name 6, 'pial': multiple matches:
some paths" and there are many files start with "rm" in the results folder. Are these standard output files? I'm considering whether these are some temporal files that should have been deleted when the whole process completed successfully.
As for the @SUMA_Make_Spec_FS, I've included the flag -NIFTI based on the suma tutorial from the afni website.
Best,
Xin