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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"
 

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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