Hi all,
Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects.
Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.” whereas the rest of the commands ran normally.
#-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
————————————————————————————————————————————————
We also tried the solution laid out in this thread with no luck: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473... https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473.html
Any help is very appreciated!
- B. Taylor Hilton Lab Data Coordinator, University of Pittsburgh
Can you send the full recon-all.log? What platform are you running on?
On 2/7/17 11:19 AM, Taylor Hilton wrote:
Hi all,
Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects.
Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.” whereas the rest of the commands ran normally.
#-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
————————————————————————————————————————————————
We also tried the solution laid out in this thread with no luck: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473...
Any help is very appreciated!
- B. Taylor Hilton
Lab Data Coordinator, University of Pittsburgh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes I’ll attach it here. I’m using a linux server(Ubuntu).
On Feb 7, 2017, at 12:32 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Can you send the full recon-all.log? What platform are you running on?
On 2/7/17 11:19 AM, Taylor Hilton wrote:
Hi all,
Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects.
Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.” whereas the rest of the commands ran normally.
#-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=4E2gE66k%2B747OnpEjef%2Baz5Z3DQx7Ht6qpqJVFxWom8%3D&reserved=0
————————————————————————————————————————————————
We also tried the solution laid out in this thread with no luck: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473... https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zqIKnda0hwYWkR7BguoviwK2l8Vy3aJzjBXabpTb1Zc%3D&reserved=0
Any help is very appreciated!
- B. Taylor Hilton
Lab Data Coordinator, University of Pittsburgh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=rMwRhzyVVLgwIerQL2z4tKX3Y%2BTWK8f95hV%2BFDOy9jU%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
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 Partners Compliance HelpLine at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
According to the log file, the error is that you need a new license:
GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html
On 2/7/17 12:49 PM, Taylor Hilton wrote:
Yes I’ll attach it here. I’m using a linux server(Ubuntu).
On Feb 7, 2017, at 12:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the full recon-all.log? What platform are you running on?
On 2/7/17 11:19 AM, Taylor Hilton wrote:
Hi all,
Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects.
Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.” whereas the rest of the commands ran normally.
#-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017
To report a problem, see *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=4E2gE66k%2B747OnpEjef%2Baz5Z3DQx7Ht6qpqJVFxWom8%3D&reserved=0
————————————————————————————————————————————————
We also tried the solution laid out in this thread with no luck: *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473... https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zqIKnda0hwYWkR7BguoviwK2l8Vy3aJzjBXabpTb1Zc%3D&reserved=0
Any help is very appreciated!
- B. Taylor Hilton
Lab Data Coordinator, University of Pittsburgh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
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 Partners Compliance HelpLine at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Apologies, that was an old log, attaching the relevant one here.
On Feb 7, 2017, at 6:02 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
According to the log file, the error is that you need a new license:
GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html&data=01%7C01%7CBTH22%40pitt.edu%7Cc8e46b2994ca49debee208d44fad662b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=w5Q7lX%2BASSB7qijJrUUV3axar1i0RN1fLXFf5izm%2F44%3D&reserved=0
On 2/7/17 12:49 PM, Taylor Hilton wrote:
Yes I’ll attach it here. I’m using a linux server(Ubuntu).
On Feb 7, 2017, at 12:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the full recon-all.log? What platform are you running on?
On 2/7/17 11:19 AM, Taylor Hilton wrote:
Hi all,
Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects.
Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.” whereas the rest of the commands ran normally.
#-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017
To report a problem, see MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=4E2gE66k%2B747OnpEjef%2Baz5Z3DQx7Ht6qpqJVFxWom8%3D&reserved=0
————————————————————————————————————————————————
We also tried the solution laid out in this thread with no luck: MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473... https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zqIKnda0hwYWkR7BguoviwK2l8Vy3aJzjBXabpTb1Zc%3D&reserved=0
Any help is very appreciated!
- B. Taylor Hilton
Lab Data Coordinator, University of Pittsburgh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=rMwRhzyVVLgwIerQL2z4tKX3Y%2BTWK8f95hV%2BFDOy9jU%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg... https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=rMwRhzyVVLgwIerQL2z4tKX3Y%2BTWK8f95hV%2BFDOy9jU%3D&reserved=0
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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 Partners Compliance HelpLine at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
can you run the commands below and tell me what happens?
cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf ln -s lh.white.preaparc.H lh.white.H
On 02/08/2017 09:44 AM, Taylor Hilton wrote:
Apologies, that was an old log, attaching the relevant one here.
On Feb 7, 2017, at 6:02 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
According to the log file, the error is that you need a new license:
GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* http://surfer.nmr.mgh.harvard.edu/registration.html
On 2/7/17 12:49 PM, Taylor Hilton wrote:
Yes I’ll attach it here. I’m using a linux server(Ubuntu).
On Feb 7, 2017, at 12:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the full recon-all.log? What platform are you running on?
On 2/7/17 11:19 AM, Taylor Hilton wrote:
Hi all,
Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects.
Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.” whereas the rest of the commands ran normally.
#-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017
To report a problem, see *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=4E2gE66k%2B747OnpEjef%2Baz5Z3DQx7Ht6qpqJVFxWom8%3D&reserved=0
————————————————————————————————————————————————
We also tried the solution laid out in this thread with no luck: *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473... https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zqIKnda0hwYWkR7BguoviwK2l8Vy3aJzjBXabpTb1Zc%3D&reserved=0
Any help is very appreciated!
- B. Taylor Hilton
Lab Data Coordinator, University of Pittsburgh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
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 Partners Compliance HelpLine at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 Partners Compliance HelpLine at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is the output: ln: failed to create symbolic link 'lh.white.H': Operation not supported
On Feb 8, 2017, at 10:38 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you run the commands below and tell me what happens?
cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf ln -s lh.white.preaparc.H lh.white.H
On 02/08/2017 09:44 AM, Taylor Hilton wrote:
Apologies, that was an old log, attaching the relevant one here.
On Feb 7, 2017, at 6:02 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
According to the log file, the error is that you need a new license:
GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com http://na01.safelinks.protection.outlook.com/" claiming to be* https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.m... https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html&data=01%7C01%7CBTH22%40pitt.edu%7C446b463cf36a4889e95708d450389542%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=CHwu5i2iSGCh56pKWyVyp3ygYwdOQ0WSEBes26448ro%3D&reserved=0
On 2/7/17 12:49 PM, Taylor Hilton wrote:
Yes I’ll attach it here. I’m using a linux server(Ubuntu).
On Feb 7, 2017, at 12:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
Can you send the full recon-all.log? What platform are you running on?
On 2/7/17 11:19 AM, Taylor Hilton wrote:
Hi all,
Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects.
Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.” whereas the rest of the commands ran normally.
#-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017
To report a problem, see *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com http://na01.safelinks.protection.outlook.com/" claiming to be* https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.m... https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting&data=01%7C01%7CBTH22%40pitt.edu%7C446b463cf36a4889e95708d450389542%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=Qjbe1jS%2BeKSdSGHHfJQKx%2FFQWrSd5B1ckHOVz9dh%2FmU%3D&reserved=0 <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.m... https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=4E2gE66k%2B747OnpEjef%2Baz5Z3DQx7Ht6qpqJVFxWom8%3D&reserved=0>
————————————————————————————————————————————————
We also tried the solution laid out in this thread with no luck: *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com http://na01.safelinks.protection.outlook.com/" claiming to be* https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg... https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html&data=01%7C01%7CBTH22%40pitt.edu%7C446b463cf36a4889e95708d450389542%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=KAGwvmXgr4Zkz%2FWWQAdxAzIrjRurig4783AvKVU3lGs%3D&reserved=0 <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg... https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zqIKnda0hwYWkR7BguoviwK2l8Vy3aJzjBXabpTb1Zc%3D&reserved=0>
Any help is very appreciated!
- B. Taylor Hilton
Lab Data Coordinator, University of Pittsburgh
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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This error suggests to me that you are mounting some external drive, or docker container, or some mix of file systems incompatible with symlinks?
Try moving the subject to a local directory
On 02/08/2017 10:41 AM, Taylor Hilton wrote:
This is the output: ln: failed to create symbolic link 'lh.white.H': Operation not supported
On Feb 8, 2017, at 10:38 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
can you run the commands below and tell me what happens?
cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf ln -s lh.white.preaparc.H lh.white.H
On 02/08/2017 09:44 AM, Taylor Hilton wrote:
Apologies, that was an old log, attaching the relevant one here.
On Feb 7, 2017, at 6:02 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
According to the log file, the error is that you need a new license:
GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com http://na01.safelinks.protection.outlook.com/" claiming to be* https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.m...
On 2/7/17 12:49 PM, Taylor Hilton wrote:
Yes I’ll attach it here. I’m using a linux server(Ubuntu).
On Feb 7, 2017, at 12:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the full recon-all.log? What platform are you running on?
On 2/7/17 11:19 AM, Taylor Hilton wrote: > Hi all, > > Having trouble with an error running "recon-all -subjid ${i} > -autorecon2” across all subjects. > > Below is where it has the error in recon-all.log. We also tried > running the last command (“ln -s …”) manually and got the error > “ln: failed to create symbolic link ‘lh.white.H’: Operation not > supported.” whereas the rest of the commands ran normally. > > #-------------------------------------------- > #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 > /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf > > mris_curvature -w lh.white.preaparc > > total integrated curvature = 18.936*4pi (237.960) --> -18 handles > ICI = 230.2, FI = 1697.2, variation=29040.790 > writing Gaussian curvature to ./lh.white.preaparc.K...done. > writing mean curvature to ./lh.white.preaparc.H...done. > rm -f lh.white.H > ln -s lh.white.preaparc.H lh.white.H > Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC > 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017 > > To report a problem, see *MailScanner has detected a possible > fraud attempt from "na01.safelinks.protection.outlook.com > http://na01.safelinks.protection.outlook.com/" > claiming to be* > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.m... > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=4E2gE66k%2B747OnpEjef%2Baz5Z3DQx7Ht6qpqJVFxWom8%3D&reserved=0 > > ———————————————————————————————————————————————— > > > We also tried the solution laid out in this thread with no luck: > *MailScanner has detected a possible fraud attempt from > "na01.safelinks.protection.outlook.com > http://na01.safelinks.protection.outlook.com/" claiming to be* > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg... > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zqIKnda0hwYWkR7BguoviwK2l8Vy3aJzjBXabpTb1Zc%3D&reserved=0 > > Any help is very appreciated! > > - B. Taylor Hilton > Lab Data Coordinator, University of Pittsburgh > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > *MailScanner has detected a possible fraud attempt from > "na01.safelinks.protection.outlook.com > http://na01.safelinks.protection.outlook.com/" claiming to be* > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
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Fra: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] På vegne av Taylor Hilton Sendt: 8. februar 2017 15:45 Til: Freesurfer support list Emne: Re: [Freesurfer] recon-all issue {Disarmed}
Apologies, that was an old log, attaching the relevant one here.
On Feb 7, 2017, at 6:02 PM, Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
According to the log file, the error is that you need a new license: GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be http://surfer.nmr.mgh.harvard.edu/registration.htmlhttps://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html&data=01%7C01%7CBTH22%40pitt.edu%7Cc8e46b2994ca49debee208d44fad662b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=w5Q7lX%2BASSB7qijJrUUV3axar1i0RN1fLXFf5izm%2F44%3D&reserved=0
On 2/7/17 12:49 PM, Taylor Hilton wrote: Yes I’ll attach it here. I’m using a linux server(Ubuntu).
On Feb 7, 2017, at 12:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the full recon-all.log? What platform are you running on?
On 2/7/17 11:19 AM, Taylor Hilton wrote: Hi all,
Having trouble with an error running "recon-all -subjid ${i} -autorecon2†across all subjects.
Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …â€) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.†whereas the rest of the commands ran normally.
#-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
mris_curvature -w lh.white.preaparc
total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017
To report a problem, see MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttps://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=4E2gE66k%2B747OnpEjef%2Baz5Z3DQx7Ht6qpqJVFxWom8%3D&reserved=0
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We also tried the solution laid out in this thread with no luck: MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473...https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html&data=01%7C01%7CBTH22%40pitt.edu%7Cac260601488f4461199608d44f809d2e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zqIKnda0hwYWkR7BguoviwK2l8Vy3aJzjBXabpTb1Zc%3D&reserved=0
Any help is very appreciated!
- B. Taylor Hilton Lab Data Coordinator, University of Pittsburgh
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