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.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
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.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 forone of our analysed subjects.
Thank you for your help.
Kind regards,
Flavia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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 listhttps://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.loreto@imperial.ac.uk"mailto:f.loreto@imperial.ac.uk f.loreto@imperial.ac.ukmailto:f.loreto@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.edumailto: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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1fDZk-6lamtx0rvBPb4dTzwv3pfopU3g0W-JKt_x4pFeNXO...
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-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 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.loreto@imperial.ac.uk" <mailto:f.loreto@imperial.ac.uk> <f.loreto@imperial.ac.uk> <mailto:f.loreto@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 forone of our analysed subjects. Thank you for your help. Kind regards, Flavia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1fDZk-6lamtx0rvBPb4dTzwv3pfopU3g0W-JKt_x4pFeNXO4GPABHiBDSX5NK2cbViS7A1b3BBuX5lGfzxTefDnbmt7RgP1VM9vRyZ-NTnz4H9xNzsh7ZN5FVnWIbXway21GLiR2pjvdy-0E6WmeDTPaPEw9nX0g_3ZKGtLi0D5vR9oxBgImDZR44V2Suifr-cswZHRrfoyzjBqz10M8Z7mLtXyIJsnFdZFueq9Rjw2FV9e4CeZeQSauT57MufuFXKGdFr_sWSzFHfmylQdJNCQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 listhttps://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.loreto@imperial.ac.uk"mailto:f.loreto@imperial.ac.uk f.loreto@imperial.ac.ukmailto:f.loreto@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.edumailto: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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZjTRl9D6AExZOe3_xrAxYN-DTHi0ZWH0Sf2lhWcEqONSIL...https://secure-web.cisco.com/1fDZk-6lamtx0rvBPb4dTzwv3pfopU3g0W-JKt_x4pFeNXO4GPABHiBDSX5NK2cbViS7A1b3BBuX5lGfzxTefDnbmt7RgP1VM9vRyZ-NTnz4H9xNzsh7ZN5FVnWIbXway21GLiR2pjvdy-0E6WmeDTPaPEw9nX0g_3ZKGtLi0D5vR9oxBgImDZR44V2Suifr-cswZHRrfoyzjBqz10M8Z7mLtXyIJsnFdZFueq9Rjw2FV9e4CeZeQSauT57MufuFXKGdFr_sWSzFHfmylQdJNCQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1ZjTRl9D6AExZOe3_xrAxYN-DTHi0ZWH0Sf2lhWcEqONSIL...
Hi Flavia, Do you have access to /tmp on your system? Can you `ls /tmp`? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@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-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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 listhttps://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.loreto@imperial.ac.uk"mailto:f.loreto@imperial.ac.uk f.loreto@imperial.ac.ukmailto:f.loreto@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.edumailto: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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External Email - Use Caution
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?
Thank you. Best, Flavia
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 26 January 2021 at 17:32 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
Hi Flavia, Do you have access to /tmp on your system? Can you `ls /tmp`? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@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-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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 listhttps://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.loreto@imperial.ac.uk"mailto:f.loreto@imperial.ac.uk f.loreto@imperial.ac.ukmailto:f.loreto@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.edumailto: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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1n5x20UbnqSVkP3KCUBKhvSp5cmI25XNec_OlGrpjlxBGhO...https://secure-web.cisco.com/1fDZk-6lamtx0rvBPb4dTzwv3pfopU3g0W-JKt_x4pFeNXO4GPABHiBDSX5NK2cbViS7A1b3BBuX5lGfzxTefDnbmt7RgP1VM9vRyZ-NTnz4H9xNzsh7ZN5FVnWIbXway21GLiR2pjvdy-0E6WmeDTPaPEw9nX0g_3ZKGtLi0D5vR9oxBgImDZR44V2Suifr-cswZHRrfoyzjBqz10M8Z7mLtXyIJsnFdZFueq9Rjw2FV9e4CeZeQSauT57MufuFXKGdFr_sWSzFHfmylQdJNCQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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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
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@imperial.ac.uk Date: Tuesday, January 26, 2021 at 1:56 PM 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 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?
Thank you. Best, Flavia
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 26 January 2021 at 17:32 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
Hi Flavia, Do you have access to /tmp on your system? Can you `ls /tmp`? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@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-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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 listhttps://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.loreto@imperial.ac.uk"mailto:f.loreto@imperial.ac.uk f.loreto@imperial.ac.ukmailto:f.loreto@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.edumailto: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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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? Many thanks for your help. Best, Flavia
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 26 January 2021 at 22:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
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
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@imperial.ac.uk Date: Tuesday, January 26, 2021 at 1:56 PM 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 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?
Thank you. Best, Flavia
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 26 January 2021 at 17:32 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
Hi Flavia, Do you have access to /tmp on your system? Can you `ls /tmp`? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@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-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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 listhttps://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.loreto@imperial.ac.uk"mailto:f.loreto@imperial.ac.uk f.loreto@imperial.ac.ukmailto:f.loreto@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.edumailto: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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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?
Many thanks for your help. Best, Flavia
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 26 January 2021 at 22:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
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
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@imperial.ac.uk Date: Tuesday, January 26, 2021 at 1:56 PM 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 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?
Thank you. Best, Flavia
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 26 January 2021 at 17:32 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
Hi Flavia, Do you have access to /tmp on your system? Can you `ls /tmp`? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@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-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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 listhttps://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.loreto@imperial.ac.uk"mailto:f.loreto@imperial.ac.uk f.loreto@imperial.ac.ukmailto:f.loreto@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.edumailto: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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Hi Flavia,
At the moment, freesurfer needs access to /tmp in order to cache temporary processing files. Can you reach out to your system admin as to why you don’t have write access to /tmp, and perhaps they will grant you access?
Best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@imperial.ac.uk Date: Thursday, January 28, 2021 at 10:41 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FW: FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
External Email - Use Caution 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?
Many thanks for your help. Best, Flavia
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 26 January 2021 at 22:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
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
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@imperial.ac.uk Date: Tuesday, January 26, 2021 at 1:56 PM 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 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?
Thank you. Best, Flavia
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Hoopes, Andrew" AHOOPES@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 26 January 2021 at 17:32 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
Hi Flavia, Do you have access to /tmp on your system? Can you `ls /tmp`? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loreto, Flavia f.loreto@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-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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 listhttps://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.loreto@imperial.ac.uk"mailto:f.loreto@imperial.ac.uk f.loreto@imperial.ac.ukmailto:f.loreto@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.edumailto: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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Douglas N. Greve -
Hoopes, Andrew -
Loreto, Flavia