FreeSurfer: link to older version of fsaverage?

1

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)?

Thanks,

Pierre

2

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”?

3

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.

4

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.