Hi, Julia-
What is the output of:
afni -ver
? I wonder if it is an older version, and so that is why "-fs_setup" isn't recognized. If that is the case, you can update your local AFNI:
@update.afni.binaries -d
But it would be good to know what version of AFNI you currently have.
On a side note, we would probably recommend adding the "-NIFTI" option, for outputting the surface files in a better format.
On a separate side note, this tutorial page might offer some helpful suggestions, too:
[
afni.nimh.nih.gov]
... but that might not add so much at this point.
--pt