Re: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error

[Krystal Xiwing Yau]

External Email - Use Caution

Dear FS experts,


I would like to follow up with the matter here - the T1.mgz isn't generated so 
I cannot inspect the image as instructed by the wiki page. I have checked the 
orientation on FreeView but it's correct. Would you please kindly advise?


Thank you so much. It's been grateful to have your guidance and support.


Sincerely,

Krystal


FreeSurfer Version: 7.3.2

OS: Linux on Ubuntu 23.04



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krystal Xiwing Yau 

Sent: 29 April 2024 16:58:18
To: Freesurfer support list
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error


External Email - Use Caution

Dear FS experts,


I am encountering an error when running recon-all. I followed the FAQ 

 page to rerun the command but still not running through. Would you please 
kindly advise? The log file is attached to this email.


Thank you.


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
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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 
 .
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 
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Re: [Freesurfer] [FreeSurfer] recon-all exited with error

[Krystal Xiwing Yau]

External Email - Use Caution

Dear Yujing,


I will be using a different computer and run it again. Thank you!


Best,

Krystal


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: 22 February 2023 23:35:57
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error

Hi Krystal,

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

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krystal Xiwing Yau
Sent: Saturday, February 18, 2023 7:45 PM
To: Freesurfer support list 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
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>
 
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. 

Re: [Freesurfer] [FreeSurfer] recon-all exited with error

[Huang, Yujing]

Hi Krystal,

Can you try running recon-all without '-parallel' flag?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krystal Xiwing Yau
Sent: Saturday, February 18, 2023 7:45 PM
To: Freesurfer support list 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
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>
 
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. 

Re: [Freesurfer] [FreeSurfer] recon-all exited with error

[Huang, Yujing]

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 
 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.
___
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 
 .
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.