Hi Joanna,

Is it possible you've run out of disk space?  What's the output of `df --si`?

-Paul
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Joanna L Eckhardt <jeckhardt@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


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