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
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