Hi Krystal,
Can you try running recon-all without '-parallel' flag?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
