Hi Flavia,
Do you have access to /tmp on your system? Can you `ls /tmp`?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Loreto, Flavia
<f.lor...@imperial.ac.uk>
Date: Tuesday, January 26, 2021 at 11:29 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not
open file for writing
External Email - Use Caution
Hi Douglas,
Here is the result:
-bash-4.2$ ls -l
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
-rw-rw---- 1 floreto rds-000730 925609 Jan 17 04:02
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
Thank you.
Best,
Flavia
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve"
<dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 26 January 2021 at 16:25
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not
open file for writing
Sorry, that first one should have been
ls -l
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
left off the "t"
On 1/26/2021 10:55 AM, Loreto, Flavia wrote:
External Email - Use Caution
Dear Douglas,
Thanks for your reply. Please see below the results of those commands:
-bash-4.2$ ls -l
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno
ls: cannot access
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno: No
such file or directory
-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label
drwxrws--- 2 floreto rds-000730 4096 Jan 17 04:47
/rds/general/project/imperialapc/live/freesurfer/APC001/label
-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001
drwxrws--- 10 floreto rds-000730 4096 Jan 17 12:46
/rds/general/project/imperialapc/live/freesurfer/APC001
-bash-4.2$ ls -ld /rds/general/project/imperialapc/live/freesurfer
drwxrws--- 3 floreto rds-000730 4096 Jan 16 20:33
/rds/general/project/imperialapc/live/freesurfer
-bash-4.2$ ls -ld /rds/general/project/imperialapc/live
drwxrws--- 11 root rds-000730 8192 Jan 18 13:06
/rds/general/project/imperialapc/live
Thank you.
Best,
Flavia
From:
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of "Douglas N. Greve"
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 26 January 2021 at 15:30
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not
open file for writing
This email from dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
originates from outside Imperial. Do not click on links and attachments unless
you recognise the sender. If you trust the sender, add them to your safe
senders
list<https://secure-web.cisco.com/1k8uIv8n4Mfbh8DZmvx7sJwGsuor3hXZNK6Wfb-oxGwnrHdkEWkFdoBjerEQqhLHERzXndHTA208ZU1hOWKU8hY9OtYeeKup69Tl-_eHk0uPQd497hf_o1XF2MxlZoW3TvLPemjJu69vqXzVdzg0nyL7mk3Ga1zlbBDIn9ow-ZNYUIh4JNkJ7FClq6fsmFIC2V4ikEJvYaYP-vD3yi2WkHmB04KpQYFw_8da7ebu5eG7zWA4W9Y_l33xVgA4cGTuk3Kmv8_QrUUsjJue0l3lU1w/https%3A%2F%2Fspam.ic.ac.uk%2FSpamConsole%2FSenders.aspx>
to disable email stamping for this address.
please send the result of
ls -l
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno
ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label
ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001
ls -ld /rds/general/project/imperialapc/live/freesurfer
ls -ld /rds/general/project/imperialapc/live
On 1/26/2021 7:50 AM, Loreto, Flavia wrote:
External Email - Use Caution
Dear FreeSurfer Experts,
I am writing to kindly follow-up on my below query. Is there any chance you
could assist me?
Thank you.
Kind regards,
Flavia
From: "f.lor...@imperial.ac.uk"<mailto:f.lor...@imperial.ac.uk>
<f.lor...@imperial.ac.uk><mailto:f.lor...@imperial.ac.uk>
Date: Monday, 18 January 2021 at 13:19
To: "Freesurfer@nmr.mgh.harvard.edu"<mailto:Freesurfer@nmr.mgh.harvard.edu>
<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>
Subject: Recon-all error: CTABWriteFileASCII; could not open file for writing
Dear FreeSurfer Experts,
Version: FreeSurfer 7.0
Platform: Bash remotely through High Performance Computing (HPC) on a MacOS
Mojave
We are trying to run recon-all on T1 images but the job stops with the
following error:
Reading annotation
/rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Seg base 1000
error: Permission denied
error: CTABwriteFileASCII(/tmp/mri_segstats.tmp.APC001.lh.176.ctab): could not
open for writing
Could you please help us figuring out where is the problem? I am attaching the
script we are running and the recon-all log for one of our analysed subjects.
Thank you for your help.
Kind regards,
Flavia
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