Hello superbug,

That's funny looking stuff to be sure. Let's try a thing or two before asking you to send me data to reproduce this.

Try rerunning the command from the directory where the output for subject 003 resides:
so cd …../003
when you're there an ls command should show you FreeSurfer directories such as orig/ mri/ surf/, etc.
then run:
@SUMA_Make_Spec_FS -GIFTI -sid 003
if it fails or the output still looks lousy, rerun it as follows:

@SUMA_Make_Spec_FS -GIFTI -sid 003 -debug 1 |& tee superbug.log

then email me the entire superbug.log file and we'll take it from there. Note that the pipe redirection above '|&' is for csh/tcsh environments. If you are using bask, redirection will be different.

cheers,
Ziad