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 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
<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
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