recon-all failed to create the symbolic links. Here are the errors from
recon-all.log:
rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
ln: failed to create symbolic link 'rh.white.H': Operation not permitted
rm -f rh.white.K
ln -s rh.white.preaparc.K rh.white.K
ln: failed to create symbolic link 'rh.white.K': Operation not permitted
You can go to your subject surf/ directory
(/home/developer/guest_shared/Sub-139/surf) to check if you can manually create
the link -
ln -s rh.white.preaparc.H rh.white.H
ln -s rh.white.preaparc.K rh.white.K
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Krystal Xiwing Yau
Sent: Thursday, February 16, 2023 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error
External Email - Use Caution
Dear FreeSurfer experts,
I ran the command "recon-all -s Sub-139 -i 139.nii -all -qcache -parallel
-openmp 6" successfully in the first few hours, and exited with error before
generating all the output files. It happened to other subjects, too. The
attached file contains the whole processing steps and ended with error.
I have set SUBJECTS_DIR to the shared folder, which was mounted in FreeSurfer
beforehand. Then, the data for analysis was copied to the Desktop. I typed in
the command and it exited with error in the end, though. Would somebody kindly
advise how to fix it, please? Your help would be highly appreciated!
OS: Windows 11
VM: ubuntu 18
Regards,
Krystal
Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
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