@SUMA_Make_Spec_FS Error Message

Hi everyone,

I’m trying to create afni datasets from my freesurfer outputs using @SUMA_Make_Spec_FS but running into an error:

-sid ${subject}
-fspath ${SUBJECTS_DIR}/fs/${subject}

I’m getting this error message from that:
" Here’s hoping these excerpts from ‘@SUMA_Make_Spec_FS -help’ enlighten:
‘-extra_fs_dsets AA BB CC …’
‘-set_space SPACE: Set the space flag of all volumes to’
‘-fspath PATH : path to ‘surf’ and ‘orig’ directories’

invalid option: ‘-fs_setup’
program failure: exiting…

cp: No match.
cp: No match.
cp: No match.
cp: /Users/username/Desktop/merp/freesurfer/1001/fs/1001/SUMA/T1.nii: No such file or directory"

-fs_setup shouldn’t be an invalid option… any thoughts?

I’m running this on a OS Catalina Version 10.15.6

Thank you in advance for any help and insight!

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:
… but that might not add so much at this point.


Thank you! Updating AFNI is all it took to get it to work, and thank you for the tip on adding the -NIFTI option.

Thank you again,