External Email - Use Caution
Hi Paul,
That was definitely the issue! I had originally shared that folder between
Windows and Ubuntu because it was in the tutorial for setting up VM, but I
changed the directory to a non-shared folder, and recon-all finished without
error.
Thank you Paul and R for all of your help!
All my best,
Joanna
--
Joanna Eckhardt
Neurosciences Graduate Program
University of California, San Diego
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wighton, Paul
<pwigh...@mgh.harvard.edu>
Sent: Friday, May 6, 2022 11:59 AM
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"
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-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 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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wighton, Paul
<pwigh...@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-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://secure-web.cisco.com/1_JhxDJbmXm1R5kwTVdWV00odXUBY8a5DcnJto4sDGg4xWnC6u3lZ5iiaS7YqiSk6iqDMoVn0GmOfqngBMoMWocN7UIbh9gfauf6kXB-J5BIsZd8sF5PIst30sYdlp4BUjYufavszDpDMfbbmo1nbB1jaF0RDIPaSbnWEBK91pQwLd_vLCv-4xmkeMtIjL7J4fvaTkDffSyEbBwRMGPlv_z11ruUskjtiAf_Y9ice8cqBcSFaGUdboeO4TEdlDfS3stzKCESgy2SOwmFL_QSgMArfOgHwXYFtUCdCw83UyOroEPQ6yyb-P_VWEtclou1T/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting<https://secure-web.cisco.com/1eto5H5j6a5mQSRzb1kPAwEMAue8-VgNNLWS-JLQaPLHmAuJQm6V_koObFANlXVvmK0e00TQR432EymIhqic3sxwJKCu__lxdrmYluXt3JywGcVwFQELFAl_tEKu_hMj2MFOR-NY12hL4puvSP_uMbk0NQn8WFwio-MJx-ikRZUnSovI2Fz9pqlBIHJ7-DAWaadalm2WC_n23a1g0VLqfwjI4tljt0oDWszkHSg5b-qlFlOAhRkpGc0fNqCKRF8u0Ai6LBU4vEHIY_vy8cNo2z3Q97uwaIEE-m3N-YegBSeghKpEIxZuy1GPiRUJl6bIF/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1mX0S-5F1U9rFCbkiVp0N-5FPcm4q-5FokK0Skpv-2DzzF13uuNL5JY50TzOGA-5Fz1jtxyWeo5lV2myg1ka02lMf6o7Ee1CRDSQY-2DTRDBT8-2DYW-5FgMQNaB0yY79dBgw0EbWLaAwNonTm1AzojTpHHFEEZYrFteKaDv8g9QjJzZKMKiv4mPN-5FDkQYnELk9S8zSC0k-5F94yK0gaRXNRi3WeOKeLIDJJzfyuB-2Dm4pIE0TmbBvTQSJCwQmqPxWCu-5FG93xbAbhZ9gTeCRVPLebKSxuqH5oAeHthCQaNQ2WQ7abJfxT52-5F4el1wAP0slKqEWf02cTn9rqkoX58_https-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fsecure-2D2Dweb.cisco.com-5F1qOeaquoMOTkikWpYGZ4Zmm7T4aU7IdoLWz-2D5FR7WjwgxWoQGxY3cPBUDVV4WjL1HTzvXW83WzudLxHfUxd3VMjIW-2D5FonAfNPXVndE-2D2DtaWDHNlTvxXSVt2XAWWGqV2-2D5FtqFc6xj1PgghG-2D2DvQD5NzYL7fMWU0fWUyVO3gu-2D2DhnNg-2D2DNlw0SYtMFHU1Mpf-2D5FezbHxFnHKFMhZR7-2D2DV9ztKJPq48qnxSxdaYp3f90UN5PtdDDL-2D5FYToCmUoLNZzThrPogT-2D2DMkRuyqenk7hzKn-2D2Dvnr1u89-2D2DjcjkzLqvD1Zlp4rCTKFLJ1mv-2D2DWZ7GImSBJ-2D2Dq-2D5F-2D2DejSRyOeOLlCao4-2D5FRYJXLprXzFkq51bQ-5Fhttp-2D253A-2D252F-2D252Fsurfer.nmr.mgh.harvard.edu-2D252Ffswiki-2D252FBugReporting-2526d-253DDwMFAg-2526c-253D-2D35OiAkTchMrZOngvJPOeA-2526r-253DVOzaW5NbE-2Dma6Pc9pAKE20dZgxgmYGpxFACLfTD0LGQ-2526m-253DTt-5FOQmgivGZKdychcXZS8aYKY019srF-5FYPdbXpJmkvyZM1-5Fuzkw7WaXxVf77AfB2-2526s-253D7PYLDUC0bc3JEa0oLNpToB7Njy6ugas78U41yjrUCYQ-2526e-253D%26d%3DDwMFAw%26c%3D-35OiAkTchMrZOngvJPOeA%26r%3DVOzaW5NbE-ma6Pc9pAKE20dZgxgmYGpxFACLfTD0LGQ%26m%3D8K3vaoIHnrR0XqbOE9Dl8E2P9zLIzLqZEpPELZLJGtWeNzwnPyMx7ijotjDIP-id%26s%3DZJPS0ZJ2usdrzFhEAeMcxgXaFN7eT6cd_Y0l0gAsHiM%26e%3D>
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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