Hi Krystal,

Can you try running recon-all without ‘-parallel’ flag?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Krystal Xiwing Yau
Sent: Saturday, February 18, 2023 7:45 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error

        External Email - Use Caution        

Dear Yujing,

Thank you for spotting it out. I have re-run recon-all in the end as to ensure all folders were generated in FreeSurfer. However, I still got the same message - the two symbolic links existed in "surf" folder, though. Would you please kindly advise what the problem is? Enclosed herewith is the recon-all.log for your reference.

Thank you very much!

Best regards,

Krystal

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Sent: 17 February 2023 01:47:15
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error

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

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