afni.nimh.nih.gov

OK,

Can you rerun the @SUMA_Make_Spec_FS command but add the option -GIFTI ?

Is the result any different with the new option?

If you are still having a bad alignment, I will need you to upload the entire FreeSurfer directory for that subject because I will need to run the @SUMA_Make_Spec_FS command locally to debug this.

Send me an email if you need instructions for uploading an archive with the necessary data.

cheers,
Ziad