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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

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