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
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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [FreeSurfer] recon-all exited with error
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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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