I can report some success with v2.2.1. The REN files for aparc and a2009 populate fine. However, it does not appear to grab the lausanne flag to make the new lausanne atlas REN files. The lausanne atlas is a further parcellation of a2009.

The command I run is:

e.g., @SUMA_Make_Spec_FS -extra_annot_labels lausanne2008_aparc -NIFTI -fs_setup -sid 1130911


In the past, I edited the original @SUMA_Make_Spec_FS program to include the lausanne file: e.g.,

set other_candidates = ( T1 aparc+aseg lausanne2008_aparc+aseg aparc.a2005s+aseg aparc.a2009s+aseg aseg.auto aseg brain.finalsurfs brain brainmask.auto brainmask norm nu nu_noneck lh.ribbon rh.ribbon wm.asegedit wm wm.seg )

and another part of the script to add "other" candidate lausanne2008_aparc.

This would make .nii from the .mgz. That old @SUMA version did not have the -extra_annot_labels flag.

But the new flag seems to be trying to do this in a more straightforward way, so I think I'm just not telling it something it needs.

I made the lausanne atlas using freesurfer commands. In the FS label folder, the following files are available:

lh.lausanne2008_aparc.annot
lh.lausanne2008_aparc_label.annot
rh.lausanne2008_aparc.annot
rh.lausanne2008_aparc_label.annot

Is there anything else I should add to the @SUMA_Make_Spec_FS command, or should I try editing the original program to look for the lausanne files as I did before?