That should not be the case, though we should start by defining what you mean by native space. The -GIFTI option should result in a volume that is in the same space as what you passed to FreeSurfer. If that is not the case then I will need to take a look at the case you have. For that I would need you to send me the output of the FreeSurfer run for that subject. If you want to try this route send me an email and we can take it from there.
The other option is to run @SUMA_AlignToEperiment to bring whatever is in the SUMA directory into alignment with any other version of that same subject's anatomy.
cheers,
Ziad
