Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
I think the latest version of FSL has this sorted out (it doesn't change your machine's POSIXLY_CORRECT setting except briefly in the middle of fsl_sub). Peace, Matt. From: chenchunhuichina chenchunhuich...@gmail.com Date: Friday, November 1, 2013 2:55 AM To: Matt Glasser m...@ma-tea.com Cc: free surfer freesurfer@nmr.mgh.harvard.edu Subject: ERROR: comparison in expression (FS with SGE) Dear Matt and freesurfers, I am encounting this old problem, that is, using fsl_sub to launch FreeSurfer jobs in SGE and get this error message: (standard_in) 2: Error: comparison in expression and freesurfer stoped. But running freesurfer without fsl_sub is OK (using fsl_sub to launch other commonds also fine). Following Matt's message on this problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-May/023961.html, I added a line POSIXLY_CORRECT=0 in fsl_sub under the line set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*` which now looks like this ... set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*` POSIXLY_CORRECT=0 ... However, the error was still the same, and what's even worse is that seems the job was launched twice. So can Matt or anybody tell me why? Am I misunderstood Matt's message? or mybe version differences since Matt's solution came out one year ago? I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0, FMRIB Software Library, Release 5.0 (c) 2012 there are two fsLsub ./src/sgeutils/fsl_sub ./bin/fsl_sub which one should I edit or both? Any help is appreciated, Thank you all! 2013-11-01 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ___ 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.
Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
Rather one unsets it like this: unset POSIXLY_CORRECT Peace, Matt. -Original Message- From: Matt Glasser [mailto:m...@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:m...@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-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@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 fis...@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 fis...@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 SGEMaybe 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 fis...@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
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:m...@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-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@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 fis...@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 fis...@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 SGEMaybe 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 fis...@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. -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive
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-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@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 fis...@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 fis...@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 SGEMaybe 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 fis...@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. -- 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 ___ Freesurfer mailing list
Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
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 fis...@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 fis...@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. -- 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
Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
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 fis...@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 SGEMaybe 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 fis...@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 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.
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 fis...@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 fis...@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 SGEMaybe 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 fis...@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. -- 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
[Freesurfer] ERROR: comparison in expression (FS with SGE)
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.
Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
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 ___ 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.
