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
Sulci recognition, error message
- riviere
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Re: Sulci recognition, error message
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
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
-
- Posts: 2
- Joined: Tue Sep 13, 2011 12:32 pm
Re: Sulci recognition, error message
Hi Denis,
thanks a lot for your quick reply. I will wait for your next reply.
Thanks in advance
Yasser
thanks a lot for your quick reply. I will wait for your next reply.
Thanks in advance
Yasser
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: Sulci recognition, error message
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
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
Re: Sulci recognition, error message
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
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
Re: Sulci recognition, error message
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)
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)