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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