anatomist problem.

Questions about Anatomist manipulation

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khi
Posts: 9
Joined: Tue Jul 13, 2004 9:37 am

anatomist problem.

Post by khi »

I used a anatomist well.
But suddenly, ( really suddenly! ) anatomist can't display image, and mesh at all.
Error message is like that.
-----------------------------------------------------------------------------------------------------
in Anatomist Show Mesh 1 gaierror: (-2, 'Name or service not known')

neuroProcesses.py (1003) in _processExecution: result = process.execution( self )
AnatomistShowMesh.py (40) in execution:
return Anatomist.AnatomistMeshView( self.read )
Anatomist.py (2057) in __init__:
self.anatomist = anatomist()
Anatomist.py (1995) in anatomist:
Anatomist.instance = Anatomist()
Anatomist.py (923) in __init__:
self.launch()
Anatomist.py (939) in launch:
port = self.comm.findFreePort()
Anatomist.py (249) in findFreePort:
res = tmpsocket.connect_ex( ( self.dest, startport ) )
-------------------------------------------------------------------------------------------------------

Because of that error, I tried to uninstall SHFJ~ package ( remove whole brainvisa directory after reading README file )
ANd I installed BrainVISA again. But still, anatomist don't run well.
And, although I remove brainvisa directory ( uninstall ) , some information must not be removed perfectly.
When I run brainvisa which is installed newly, prior database information still remain.

Because I can't execute anatomist, I can't confirm any images and mesh ^^;
Please help me~

Thank you~
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riviere
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Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Post by riviere »

It seems that the connection between BrainVisa and Anatomist broke and can't be established anymore. They communicate via a (local) network connection. Have you changed anything in your networking configuration (IP address, machine name etc) ?
Anatomist itself is not broken I think: you should still be able to run anatomist directly (without brainvisa)
You can try rebooting the machine: something seems to be going wrong in the network services. You can also try a "ping localhost" to see if the local network access (name service etc) is working or not.

When you uninstall the package, your personal configuration files are not removed (of course) so you can keep your config (database and options) when you install a newer version.

Denis
khi
Posts: 9
Joined: Tue Jul 13, 2004 9:37 am

khi

Post by khi »

Thank you for your reply.

As you said, anatomist itself run.
But, image and mesh can't be visualized. ( empty white window without object )
Rebooting the machine was not able to recover anatomist.
If uninstall is done perfectly, is it possible to use anatomist normally with new brainvisa ?
I wanna try that and I wonder where personal configuration files exist.

I ask a favor of you for replying.

Thank you~
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riviere
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Post by riviere »

Well, I don't think there would be something in the config files that could explain your problem - I rather suspect some change in your system. Anyway you are free to try: Anatomist personal data is in the directory $HOME/.anatomist and BrainVisa uses $HOME/.brainvisa
The configurations are, more precisely, $HOME/.anatomist/config/settings.cfg and $HOME/.brainvisa/options.py
If you are using BrainVisa/Anatomist on a Windows system, then the home directory is given by the environment variable USERPROFILE rather than HOME.
As you said, Anatomist used to work and doesn't anymore - that's strange, the programs themselves can't have changed. Are you sure nothing changed in your system ? Maybe your sysadmin has upgraded your machine or something ? Which system are you using ?

Denis
khi
Posts: 9
Joined: Tue Jul 13, 2004 9:37 am

anatomist

Post by khi »

Thank you for reply.

For reinstall, I deleted all package directory including .anatomist and .brainvisa directory.
But as you said, reinstalling new brainvisa package was useless.
It's difficult to understand ~.
Although system has changed, I thought that newly installed brainvisa can be fit for new system. But it can't .
My system is Redhat Linux 9.0 and I haven't changed system for myself.
After set up brainvisa, just a few programs has installed. ( acrobat reader, kdevelop3.0 and VTK.. and so on.. ? )
Is there a possibility to make a change which can affect anatomist by installing other programs ?
What change of system can affect brainvisa software package ?

Please could you reply it ?

Thank you~
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riviere
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Post by riviere »

We are developing mainly on RedHat 9 so everything should work well (even if the binary packages are built on RedHat 7.3 to remain compatible with older Linuxes).
The critical system part for Anatomist is the 3D card support: many 3D cards have incomplete or buggy drivers on Linux, so you may have to check this: Nvidia and ATI provide drivers and OpenGL libraries suitable for their cards (I never tried ATI's drivers to be honest), and I have no experience with other cards.
Otherwise, as it appeared that the network connection between BrainVisa and Anatomist couldn't be established, there might be something in the networking system which is not installed (but I'm a bit surprised, I think the loopback network device is used by many system parts, including the X server).

Denis
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