Hi Joanna,
Is it possible you've run out of disk space? What's the output of `df --si`?
-Paul
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Joanna L Eckhardt
<jeckha...@health.ucsd.edu>
Sent: Friday, May 6, 2022 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link
'lh.white.H': Operation not permitted"
External Email - Use Caution
Dear FreeSurfer Team,
I am attempting to run Recon-all on practice cannabis data on the tutorial,
using Ubuntu18 VM for Windows os (also I completely new to coding and Ubuntu).
On my first attempt to run Recon-all, I got the error shown below: "ln: failed
to create symbolic link 'lh.white.H': Operation not permitted."
mris_curvature -w -seed 1234 lh.white.preaparc
setting seed for random number generator to 1234
total integrated curvature = 25.993*4pi (326.639) --> -25 handles
ICI = 146.8, FI = 1524.9, variation=23628.367
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
@#@FSTIME 2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M
144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08
@#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub101-sesBL exited with ERRORS at Thu May 5 23:34:17 EDT 2022
For more details, see the log file
/home/developer/guest_shared/fs-subjects/sub101-sesBL/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://secure-web.cisco.com/1qOeaquoMOTkikWpYGZ4Zmm7T4aU7IdoLWz_R7WjwgxWoQGxY3cPBUDVV4WjL1HTzvXW83WzudLxHfUxd3VMjIW_onAfNPXVndE-taWDHNlTvxXSVt2XAWWGqV2_tqFc6xj1PgghG-vQD5NzYL7fMWU0fWUyVO3gu-hnNg-Nlw0SYtMFHU1Mpf_ezbHxFnHKFMhZR7-V9ztKJPq48qnxSxdaYp3f90UN5PtdDDL_YToCmUoLNZzThrPogT-MkRuyqenk7hzKn-vnr1u89-jcjkzLqvD1Zlp4rCTKFLJ1mv-WZ7GImSBJ-q_-ejSRyOeOLlCao4_RYJXLprXzFkq51bQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>
After searching through the archives, I see that other people have had the same
problem in that their os is not able to create a symbolic link. I tried
following one of the archives and did:
developer@developer-VirtualBox:~/guest_shared/mv-ds000174-1.0.1-Cannabis/sub-101/ses-BL/anat$
cd /home/developer/guest_shared/fs-subjects
developer@developer-VirtualBox:~/guest_shared/fs-subjects$ ln -s
/home/developer/guest_shared/fs-subjects/fsaverage
ln: failed to create symbolic link './fsaverage': Operation not permitted
But I again received the "failed to create symbolic link. How can I allow
symbolic links? Also, I was generally wondering how do you rerun recon-all
starting from a specific step once I get this working? Does one have to rerun
all of recon-all each time there is an error or can I start from where I left
off?
Thank you so much for your help!
Best wishes,
Joanna
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