Dear Shadia,

There are 2 spots in recon-all where symbolic link is created.

The first you can overcome by:
find following line in your recon-all:

set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix)
and replace it by
set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix)

The second you overcome by copying the directory  $FREESURFER_HOME/subjects/fsaverage and all its contents of to your $SUBJECTS_DIR.

Then rerun recon-all on your subject.

Antonin Skoch


Hello all,

I'm having trouble with recon-all on a Linux server, I'm running into the following error for all of my subjects:

.....
mris_curvature -w lh.white.preaparc

total integrated curvature = 6.657*4pi (83.654) --> -6 handles
ICI = 129.9, FI = 1309.2, variation=20703.115
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: creating symbolic link `lh.white.H': Operation not supported
Linux bsrv10 ..... #1 SMP Tue Nov 15 14:13:21 CST 2016 x86_64 x86_64 x86_64 GNU/Linux

I've tried to create a symbolic link as suggested in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040476.html , but I still get a message saying operation not supported

ln -s /usr/local/freesurfer/subjects/fsaverage /home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia
ln: creating symbolic link `/home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia/fsaverage': Operation not supported


I've also tried to manually create the symbolic link in that last line: ln -s lh.white.preaparc.H lh.white.H
But again it says operation not supported.

Recon-all log: attached
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c  

Any advice?

Thank you

Shadia