@SUMA_Make_Spec_FS Error Message

AFNI Message Board
1

Hi everyone,

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

@SUMA_Make_Spec_FS
-fs_setup
-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!
Julia

2

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:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fs/fs_fsprep.html
… but that might not add so much at this point.

–pt

3

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,
Julia