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 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 >>>> <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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
