FreeSurfer: link to older version of fsaverage?

Dear all,

I have tried to use the latest version of FreeSurfer (v7.1.1) on Baobab. The recon-all pipeline crashes with an error message that reads,

Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!
The fsaverage link probably points to an older freesurfer version

Indeed, in my file manager, when I browse the SUBJECTS_DIR, the link to fsaverage reads link to /opt/ebsofts/Core/FreeSurfer/6.0.0-centos6_x86_64/subjects/fsaverage

I’m not sure when this link is established, but it might a problem if it does not conform to the precise version of FreeSurfer that a user might want to use. Can the link be changed (e.g. by the user)?



Hi, as I don’t know how FreeSurfer is working, I’m only guessing.

[sagon@login1.yggdrasil ~]$ ml FreeSurfer/7.1.1-centos7_x86_64
[sagon@login1.yggdrasil ~]$ ls -lad $SUBJECTS_DIR
drwxr-xr-x 14 root root 4096 Jul 23  2020 /opt/ebsofts/FreeSurfer/7.1.1-centos7_x86_64/subjects

Were is “the link to fsaverage”?

Sorry, here is a little bit more background. FreeSurfer stores all its output in a directory defined by SUBJECTS_DIR. Within this directory, there should always be a “subject” called fsaverage. In the SUBJECTS_DIR that I created in my home disk space, there is a symbolic link to fsaverage whose address points to version 6.0.0 of FreeSurfer, and does not update when I module load FreeSurfer 7.1.1. I guess I’ll simply update this symbolic link manually.

If the symbolic link was done by yourself or while running FreeSurfer and is in your home directory, yes you should update it manually I guess.