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/14hambhZcwlHm-TUI0wi8GmzTNRhNjDTjrHO81ZQzO0DprnW0ojx5KD-LTyISI4jeDK03AwgiBl28UP0y9ABz9oQu4W7oS_NXfwjPp6LAouUz1f4eSYthZ_hC_Xe6Ssi4Jbhohpaz2cc4oBujQeDBrB7o9HpBeXAJV9SzelG8_1cSCHJ_xDzXjoivdxgRhqq_UPMkj0_euOS5YUjLZnbqxrX5JdxoaKJ9H8_hEnI86Itt0-mKyyac6YBC_6s2dtm9erpXBai63ObIhSxSauL2NgayuNw4CWfUE9yEZNy-Ilh16UGedwBKUUuMLrwJ259C/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting<https://secure-web.cisco.com/1mX0S_1U9rFCbkiVp0N_Pcm4q_okK0Skpv-zzF13uuNL5JY50TzOGA_z1jtxyWeo5lV2myg1ka02lMf6o7Ee1CRDSQY-TRDBT8-YW_gMQNaB0yY79dBgw0EbWLaAwNonTm1AzojTpHHFEEZYrFteKaDv8g9QjJzZKMKiv4mPN_DkQYnELk9S8zSC0k_94yK0gaRXNRi3WeOKeLIDJJzfyuB-m4pIE0TmbBvTQSJCwQmqPxWCu_G93xbAbhZ9gTeCRVPLebKSxuqH5oAeHthCQaNQ2WQ7abJfxT52_4el1wAP0slKqEWf02cTn9rqkoX58/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_1qOeaquoMOTkikWpYGZ4Zmm7T4aU7IdoLWz-5FR7WjwgxWoQGxY3cPBUDVV4WjL1HTzvXW83WzudLxHfUxd3VMjIW-5FonAfNPXVndE-2DtaWDHNlTvxXSVt2XAWWGqV2-5FtqFc6xj1PgghG-2DvQD5NzYL7fMWU0fWUyVO3gu-2DhnNg-2DNlw0SYtMFHU1Mpf-5FezbHxFnHKFMhZR7-2DV9ztKJPq48qnxSxdaYp3f90UN5PtdDDL-5FYToCmUoLNZzThrPogT-2DMkRuyqenk7hzKn-2Dvnr1u89-2DjcjkzLqvD1Zlp4rCTKFLJ1mv-2DWZ7GImSBJ-2Dq-5F-2DejSRyOeOLlCao4-5FRYJXLprXzFkq51bQ_http-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FBugReporting%26d%3DDwMFAg%26c%3D-35OiAkTchMrZOngvJPOeA%26r%3DVOzaW5NbE-ma6Pc9pAKE20dZgxgmYGpxFACLfTD0LGQ%26m%3DTt_OQmgivGZKdychcXZS8aYKY019srF_YPdbXpJmkvyZM1_uzkw7WaXxVf77AfB2%26s%3D7PYLDUC0bc3JEa0oLNpToB7Njy6ugas78U41yjrUCYQ%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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