Sulci recognition, error message

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yasseraleman
Posts: 2
Joined: Tue Sep 13, 2011 12:32 pm

Sulci recognition, error message

Post by yasseraleman »

Morphologist --> Sulci --> Recognition --> Sulci Recognition (Both Hemispheres)

Hello everybody,

I have recently installed Brainvisa 4.4 (brainvisa-Mandriva-2008.0-x86_64-4.4.0-2013_11_18.tar) and I am getting error messages during Sulci recognition process. My OS is Ubuntu 13.04

All Morphologist (2013) steps ran without errors but when the sulci recognition started I have got this error message.
The SPAM models are correctly installed (Brainvisa finds them).

Process Sulci Recognition (both hemispheres) started on 2014/08/29 12:55
/usr/local/brainvisa/share/brainvisa-share-4.4/nomenclature/syntax/graph.stx: found "" while waiting for "*BEGIN" (line 838) : , line 838
Traceback (most recent call last): File "/usr/local/brainvisa/scripts/sigraph/sulci_registration/independent_tag_with_registration.py", line 467, in <module>

if __name__ == '__main__' : main() File "/usr/local/brainvisa/scripts/sigraph/sulci_registration/independent_tag_with_registration.py", line 385, in main graph = io.load_graph(options.transfile, options.input_graphname) File "/usr/local/brainvisa/python/sulci/common/io.py", line 40, in load_graph return load_graphs(transfile, [graphname], label_mode)[0] File "/usr/local/brainvisa/python/sulci/common/io.py", line 35, in load_graphs ft.translate(g, label_mode, label_mode) TypeError: FoldLabelsTranslator.translate(): argument 1 has unexpected type 'Graph'


Any idea ??

Best regards
Yasser
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riviere
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Location: CEA NeuroSpin, Saint Aubin, France
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Re: Sulci recognition, error message

Post by riviere »

Hi,
I thought I fixed this problem by the time I compiled on Ubuntu 13.04 and later releases, but I thought it was a compilation-time issue and did not think it could also be a runtime problem in low-level stream reading routines. I have to check that.
Denis
yasseraleman
Posts: 2
Joined: Tue Sep 13, 2011 12:32 pm

Re: Sulci recognition, error message

Post by yasseraleman »

Hi Denis,

thanks a lot for your quick reply. I will wait for your next reply.

Thanks in advance
Yasser
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riviere
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Location: CEA NeuroSpin, Saint Aubin, France
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Re: Sulci recognition, error message

Post by riviere »

Well, I have no Ubuntu 13.04 at reach now, but I have tried the brainvisa-Mandriva-2008.0-x86_64-4.4.0-2013_11_18 binary distribution with two Ubuntu 14.04 systems, and it seemed to work with no error, so I cannot reproduce the problem now.

the first message you get, 'graph.stx: found "" while waiting for "*BEGIN" (line 838) : , line 838', reminds me a problem I fixed that I mentioned yesterday. I am still surprised to see it here. The second error message, "TypeError: FoldLabelsTranslator.translate(): argument 1 has unexpected type 'Graph' " could be related to the first one, or be due to a missing plugin in our libraries (but I have no idea why it would be missing).

I am a bit puzzled, here...

Denis
coday
Posts: 1
Joined: Thu Sep 25, 2014 7:00 am

Re: Sulci recognition, error message

Post by coday »

Hallo I get the same error doing sulci recognition: "graph.stx: found "" while waiting for "*BEGIN" (line 838) :"

I haven't been able to find out why. And you say you might have a fix for it?

I am running brainvisa 4.4.0 on Ubuntu 12.04 in a virtualbox.

Kind regards
SylvainT
Posts: 73
Joined: Mon Feb 13, 2006 6:37 pm
Location: INT, Marseille, France

Re: Sulci recognition, error message

Post by SylvainT »

Hi everybody,

Denis, we came across this same problem in a weird situation and we managed to "solve" it... This might help you diagnose the problem...

Soooooooooooo, following my question here and your answer to do as indicated in this thread, I removed the brainvisa libstdc++ and we were using the freesurfer toolbox successfully... But then, we got the error described above when attempting to do sulci recognition! So I put back the libstdc++ in its original location, and the sulci recognition problem is gone...

Hope this helps...

Cheers,

Sylvain (working on debian wheezy)
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