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: [log in to unmask]

[mailto:[log in to unmask]] On Behalf Of Xue, Feng

Sent: Sunday, March 14, 2010 1:37 PM

To: Bruce Fischl

Cc: [log in to unmask]

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

<[log in to unmask]> 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

>> <[log in to unmask]> 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

>>>> <[log in to unmask]> 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

>>>>>> [log in to unmask]

>>>>>> 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

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and

>>>>> properly

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>>>>> 

>>>>> 

>>>> 

>>>> 

>>>> 

>>> 

>> 

>> 

>> 

> 

-- 

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

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