Hmm, ok that's not the issue.  You have plenty of free disk space (185Gb)

Is the folder /home/developer/guest_shared shared with the host OS (windows)? That could be the issue as windows does not support symbolic links.  Could you try changing the subject's directory to something that is not shared with the host OS?  

e.g:
```
mkdir -p /home/developer/fs-subjects
export SUBJECTS_DIR=/home/developer/fs-subjects
```

And then try running recon-all again?

My apologies.  This is my fault as I originally suggested that location for the subjects directory. Also, thanks to R. for his help diagnosing this issue!

-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 2:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"
 

        External Email - Use Caution        

Hi Paul, 

I have everything on my Data (D:) drive because my OS (C:) drive was already nearly full when I began this process of downloading FreeSurfer and knew it wouldn't have enough space. Is that a problem that I am using the D: drive? (I am not too familiar with the differences between the two). 

Pasted below is the output of df --si.

Thank you for your help!
Joanna
developer@developer-VirtualBox:~/guest_shared/fs-subjects$ df --si
Filesystem      Size  Used Avail Use% Mounted on
udev            4.2G     0  4.2G   0% /dev
tmpfs           835M  1.6M  833M   1% /run
/dev/sda1       216G   21G  185G  10% /
tmpfs           4.2G     0  4.2G   0% /dev/shm
tmpfs           5.3M  4.1k  5.3M   1% /run/lock
tmpfs           4.2G     0  4.2G   0% /sys/fs/cgroup
/dev/loop0       69M   69M     0 100% /snap/gtk-common-themes/1519
/dev/loop1      230M  230M     0 100% /snap/gnome-3-34-1804/72
/dev/loop3       47M   47M     0 100% /snap/snapd/15534
/dev/loop2       46M   46M     0 100% /snap/snapd/15177
/dev/loop6      787k  787k     0 100% /snap/gnome-characters/726
/dev/loop5      2.8M  2.8M     0 100% /snap/gnome-calculator/920
/dev/loop4      787k  787k     0 100% /snap/gnome-characters/741
/dev/loop7      230M  230M     0 100% /snap/gnome-3-34-1804/77
/dev/loop9      254M  254M     0 100% /snap/gnome-3-38-2004/70
/dev/loop8      2.8M  2.8M     0 100% /snap/gnome-system-monitor/174
/dev/loop10      66M   66M     0 100% /snap/core20/1434
/dev/loop11     132k  132k     0 100% /snap/bare/5
/dev/loop12      69M   69M     0 100% /snap/gtk-common-themes/1515
/dev/loop13     656k  656k     0 100% /snap/gnome-logs/106
/dev/loop15      59M   59M     0 100% /snap/core18/2128
/dev/loop14     2.7M  2.7M     0 100% /snap/gnome-system-monitor/163
/dev/loop16     261M  261M     0 100% /snap/gnome-3-38-2004/99
/dev/loop17      59M   59M     0 100% /snap/core18/2344
/dev/loop18     2.7M  2.7M     0 100% /snap/gnome-calculator/884
/dev/loop19      66M   66M     0 100% /snap/core20/1376
tmpfs           835M   17k  835M   1% /run/user/121
tmpfs           835M   46k  835M   1% /run/user/1000
shared          1.1T   48G  953G   5% /home/developer/guest_shared


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wighton, Paul <PWIGHTON@mgh.harvard.edu>
Sent: Friday, May 6, 2022 10:55 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"
 
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