Sorry, I didn't notice that the reply address was not the list, I've done re-post it.
Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings.
It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script.
On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you post this to the list? There are others better qualified to say what's going on. But if everything finished ok is there really a problem? Maybe this is just a warning? On Sun, 14 Mar 2010, Xue, Feng wrote:
Hi Bruce,
Thanks for your reply. The recon-all.log said it finished without error. please find the whole scripts root in the attachment. I'm also running a raw testing with one subject and without SGEяяMaybe I can report the result the day after tomorrow.
BTW, I found in my 64bit Debian nodes, I repeated got the error as below (standard_in) 2: Error: comparison in expression but in 32bit, I met both.
for the GMail security restriction, I changed recon-all.cmd in the attachment to recon-all.cmds.
On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what does the recon-all.log say? Did the recon finish correctly? Does this happen if you just run it on the command line? Bruce
On Sat, 13 Mar 2010, Xue, Feng wrote:
Dear Bruce & FS experts,
Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all:
$ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression
I also checked the recon-all-status.log file, but not error was found.
Has anyone met this problem? Is it critical? Thanks in advance.
-- Best Regards
Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience
National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
if it was a syntax error then recon-all wouldn't have finished, so I'm not sure what's going on. You should visually inspect the surfaces and segmentations to make sure they are all ok.
cheers, Bruce
On Mon, 15 Mar 2010, Xue, Feng wrote:
Sorry, I didn't notice that the reply address was not the list, I've done re-post it.
Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings.
It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script.
On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you post this to the list? There are others better qualified to say what's going on. But if everything finished ok is there really a problem? Maybe this is just a warning? On Sun, 14 Mar 2010, Xue, Feng wrote:
Hi Bruce,
Thanks for your reply. The recon-all.log said it finished without error. please find the whole scripts root in the attachment. I'm also running a raw testing with one subject and without SGEÿÿÿÿMaybe I can report the result the day after tomorrow.
BTW, I found in my 64bit Debian nodes, I repeated got the error as below (standard_in) 2: Error: comparison in expression but in 32bit, I met both.
for the GMail security restriction, I changed recon-all.cmd in the attachment to recon-all.cmds.
On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what does the recon-all.log say? Did the recon finish correctly? Does this happen if you just run it on the command line? Bruce
On Sat, 13 Mar 2010, Xue, Feng wrote:
Dear Bruce & FS experts,
Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all:
$ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression
I also checked the recon-all-status.log file, but not error was found.
Has anyone met this problem? Is it critical? Thanks in advance.
-- Best Regards
Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience
National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thanks! I would check them later.
On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if it was a syntax error then recon-all wouldn't have finished, so I'm not sure what's going on. You should visually inspect the surfaces and segmentations to make sure they are all ok.
cheers, Bruce
On Mon, 15 Mar 2010, Xue, Feng wrote:
Sorry, I didn't notice that the reply address was not the list, I've done re-post it.
Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings.
It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script.
On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you post this to the list? There are others better qualified to say what's going on. But if everything finished ok is there really a problem? Maybe this is just a warning? On Sun, 14 Mar 2010, Xue, Feng wrote:
Hi Bruce,
Thanks for your reply. The recon-all.log said it finished without error. please find the whole scripts root in the attachment. I'm also running a raw testing with one subject and without SGEяяяяMaybe I can report the result the day after tomorrow.
BTW, I found in my 64bit Debian nodes, I repeated got the error as below (standard_in) 2: Error: comparison in expression but in 32bit, I met both.
for the GMail security restriction, I changed recon-all.cmd in the attachment to recon-all.cmds.
On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what does the recon-all.log say? Did the recon finish correctly? Does this happen if you just run it on the command line? Bruce
On Sat, 13 Mar 2010, Xue, Feng wrote:
Dear Bruce & FS experts,
Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all:
$ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression
I also checked the recon-all-status.log file, but not error was found.
Has anyone met this problem? Is it critical? Thanks in advance.
-- Best Regards
Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience
National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I'm dredging this 2 year old post up for the benefit of Google and anyone else who wonders about the cause of this. It is a non-fatal error (for FreeSurfer, but perhaps not other things) that is caused by having set the variable:
POSIXLY_CORRECT=1
It causes bc (on Debian/Ubuntu) systems to fail when making comparisons like:
echo '3.5 > 2.5' | bc -l
I am guessing (because this is what I was doing) that the poster was using fsl_sub to launch FreeSurfer jobs in SGE. fsl_sub sets this flag for some reason, but commenting it out seems not to cause any problems.
Peace,
Matt.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Xue, Feng Sent: Sunday, March 14, 2010 1:37 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
Thanks! I would check them later.
On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if it was a syntax error then recon-all wouldn't have finished, so I'm not sure what's going on. You should visually inspect the surfaces and segmentations to make sure they are all ok.
cheers, Bruce
On Mon, 15 Mar 2010, Xue, Feng wrote:
Sorry, I didn't notice that the reply address was not the list, I've done re-post it.
Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings.
It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script.
On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you post this to the list? There are others better qualified to say what's going on. But if everything finished ok is there really a
problem?
Maybe this is just a warning? On Sun, 14 Mar 2010, Xue, Feng wrote:
Hi Bruce,
Thanks for your reply. The recon-all.log said it finished without error. please find the whole scripts root in the attachment. I'm also running a raw testing with one subject and without
SGEяяяяMaybe
I can report the result the day after tomorrow.
BTW, I found in my 64bit Debian nodes, I repeated got the error as
below
(standard_in) 2: Error: comparison in expression but in 32bit, I met both.
for the GMail security restriction, I changed recon-all.cmd in the attachment to recon-all.cmds.
On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what does the recon-all.log say? Did the recon finish correctly? Does this happen if you just run it on the command line? Bruce
On Sat, 13 Mar 2010, Xue, Feng wrote:
Dear Bruce & FS experts,
Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all:
$ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression
I also checked the recon-all-status.log file, but not error was
found.
Has anyone met this problem? Is it critical? Thanks in advance.
-- Best Regards
Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience
National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
Another note on this:
Apparently, getopt (used in fsl_sub) doesn't work correctly when this flag is not set to 1 (it picks op a lot of options it shouldn't). Thus, instead of commenting out the flag, it is better to set it to zero after the
set -- `getopt T:q:a:p:M:j:t:N:n:Fvm:l: $*`
Line. Then one gets the best of both worlds.
Peace,
Matt.
-----Original Message----- From: Matt Glasser [mailto:matt@ma-tea.com] Sent: Thursday, March 22, 2012 5:36 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE)
I'm dredging this 2 year old post up for the benefit of Google and anyone else who wonders about the cause of this. It is a non-fatal error (for FreeSurfer, but perhaps not other things) that is caused by having set the variable:
POSIXLY_CORRECT=1
It causes bc (on Debian/Ubuntu) systems to fail when making comparisons like:
echo '3.5 > 2.5' | bc -l
I am guessing (because this is what I was doing) that the poster was using fsl_sub to launch FreeSurfer jobs in SGE. fsl_sub sets this flag for some reason, but commenting it out seems not to cause any problems.
Peace,
Matt.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Xue, Feng Sent: Sunday, March 14, 2010 1:37 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
Thanks! I would check them later.
On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if it was a syntax error then recon-all wouldn't have finished, so I'm not sure what's going on. You should visually inspect the surfaces and segmentations to make sure they are all ok.
cheers, Bruce
On Mon, 15 Mar 2010, Xue, Feng wrote:
Sorry, I didn't notice that the reply address was not the list, I've done re-post it.
Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings.
It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script.
On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you post this to the list? There are others better qualified to say what's going on. But if everything finished ok is there really a
problem?
Maybe this is just a warning? On Sun, 14 Mar 2010, Xue, Feng wrote:
Hi Bruce,
Thanks for your reply. The recon-all.log said it finished without error. please find the whole scripts root in the attachment. I'm also running a raw testing with one subject and without
SGEяяяяMaybe
I can report the result the day after tomorrow.
BTW, I found in my 64bit Debian nodes, I repeated got the error as
below
(standard_in) 2: Error: comparison in expression but in 32bit, I met both.
for the GMail security restriction, I changed recon-all.cmd in the attachment to recon-all.cmds.
On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what does the recon-all.log say? Did the recon finish correctly? Does this happen if you just run it on the command line? Bruce
On Sat, 13 Mar 2010, Xue, Feng wrote:
Dear Bruce & FS experts,
Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all:
$ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression
I also checked the recon-all-status.log file, but not error was
found.
Has anyone met this problem? Is it critical? Thanks in advance.
-- Best Regards
Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience
National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
Rather one unsets it like this:
unset POSIXLY_CORRECT
Peace,
Matt.
-----Original Message----- From: Matt Glasser [mailto:matt@ma-tea.com] Sent: Friday, May 18, 2012 12:47 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE)
Another note on this:
Apparently, getopt (used in fsl_sub) doesn't work correctly when this flag is not set to 1 (it picks op a lot of options it shouldn't). Thus, instead of commenting out the flag, it is better to set it to zero after the
set -- `getopt T:q:a:p:M:j:t:N:n:Fvm:l: $*`
Line. Then one gets the best of both worlds.
Peace,
Matt.
-----Original Message----- From: Matt Glasser [mailto:matt@ma-tea.com] Sent: Thursday, March 22, 2012 5:36 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE)
I'm dredging this 2 year old post up for the benefit of Google and anyone else who wonders about the cause of this. It is a non-fatal error (for FreeSurfer, but perhaps not other things) that is caused by having set the variable:
POSIXLY_CORRECT=1
It causes bc (on Debian/Ubuntu) systems to fail when making comparisons like:
echo '3.5 > 2.5' | bc -l
I am guessing (because this is what I was doing) that the poster was using fsl_sub to launch FreeSurfer jobs in SGE. fsl_sub sets this flag for some reason, but commenting it out seems not to cause any problems.
Peace,
Matt.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Xue, Feng Sent: Sunday, March 14, 2010 1:37 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
Thanks! I would check them later.
On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if it was a syntax error then recon-all wouldn't have finished, so I'm not sure what's going on. You should visually inspect the surfaces and segmentations to make sure they are all ok.
cheers, Bruce
On Mon, 15 Mar 2010, Xue, Feng wrote:
Sorry, I didn't notice that the reply address was not the list, I've done re-post it.
Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings.
It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script.
On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you post this to the list? There are others better qualified to say what's going on. But if everything finished ok is there really a
problem?
Maybe this is just a warning? On Sun, 14 Mar 2010, Xue, Feng wrote:
Hi Bruce,
Thanks for your reply. The recon-all.log said it finished without error. please find the whole scripts root in the attachment. I'm also running a raw testing with one subject and without
SGEяяяяMaybe
I can report the result the day after tomorrow.
BTW, I found in my 64bit Debian nodes, I repeated got the error as
below
(standard_in) 2: Error: comparison in expression but in 32bit, I met both.
for the GMail security restriction, I changed recon-all.cmd in the attachment to recon-all.cmds.
On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what does the recon-all.log say? Did the recon finish correctly? Does this happen if you just run it on the command line? Bruce
On Sat, 13 Mar 2010, Xue, Feng wrote:
Dear Bruce & FS experts,
Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all:
$ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression
I also checked the recon-all-status.log file, but not error was
found.
Has anyone met this problem? Is it critical? Thanks in advance.
-- Best Regards
Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience
National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Matt Glasser -
Xue, Feng