Hi Xixi,
Try having FreeSurfer a GIFTI version of the modified annotation file, then load it with SUMA. You should be able to perform the conversion with:
mris_convert -c lh.aparc_parula.a2009s.annot lh.aparc_parula.a2009s.annot.gii
then load the .gii dataset with SUMA much like you were trying with the ill fated output of FSread_annot.
Let me know if that does the trick and if not, which error messages you ended up with.
Also, note that you are better off using option -GIFTI with all of your new @SUMA_Make_Spec_FS commands. See the -help output for details.
cheers
Ziad