Hi Rafael,
Is your subject directory stored on an external drive like an SD card? The
“Function not implemented” error implies that symlinks are not supported on the
filesystem that you’re saving to. Ubuntu 18 definitely supports symlinks and I
see that SUBJECTS_DIR points to /media/rafa…. You should process your data on
the ubuntu filesystem first, then try copying it onto a card after.
Best,
Andrew
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rafael Espericueta
<respe...@ucsc.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, December 18, 2019 at 8:57 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error running "Test your FreeSurfer Installation"
External Email - Use Caution
I was trying to run the command: recon-all -s bert -all
It ran for hours, but finally output the following:
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Function not implemented
Linux hypatia 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC 2019
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Wed Dec 18 16:18:43 PST 2019
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 18.04.3
3) recon-all.log: see attached
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