Hi Andrew,

 

This is the output:

 

-bash-4.2$   touch /tmp/mytempfile && rm -f /tmp/mytempfile

touch: cannot touch ‘/tmp/mytempfile’: Permission denied

 

Yes, I am running it through the High Performance Computing (HPC) cluster. Is there a way to work around this kind of permission problem?

 

 

Okay, maybe it’s a permission error. How about the output of the following?

 

    touch /tmp/mytempfile && rm -f /tmp/mytempfile

 

Also, are you running recon-all on a cluster?

Andrew

 

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Hi Andrew,

Many thanks for your reply. This is what I get if I ls/temp:

 

-bash-4.2$ ls /tmp

hsperfdata_gc520

hsperfdata_rf1116

hsperfdata_scliffor

pbs.3000969.pbs

systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-gKdDDc

systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-ZujPj0

systemd-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-sX44ZN

systemd-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-ukGmwH

 

What would you recommend doing?

 

 

 

Hi Flavia,

Do you have access to /tmp on your system? Can you `ls /tmp`?

Andrew

 

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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

 

 

 

Sorry, that first one should have been
ls -l /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot
left off the "t"

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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-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 26 January 2021 at 15:30
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

 

This email from dgreve@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 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:

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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.loreto@imperial.ac.uk" <f.loreto@imperial.ac.uk>
Date: Monday, 18 January 2021 at 13:19
To: "Freesurfer@nmr.mgh.harvard.edu" <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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