linux crash report

Questions about Anatomist manipulation

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cyril
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linux crash report

Post by cyril »

Hi there,

I'm a new user of brain visa/anatomist enjoying french work .. until my linux mandriva 2006 crashed - I report the bug here and maybe someone can advise me ..

the crash happen each time I want to look at a graph of sulci; I can generate the graph but not look at it :x - even if it cannot be fixed, is there a way to get the values generated for sulci - gyri (maybe via python?)

thanks
cyril
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Jean-Francois Mangin
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Post by Jean-Francois Mangin »

You can use the morphometry treatment providing numbers... but it would be a very bad idea. I do not advise anybody to deal with sulcal morphometry without carefully controlling the behaviour of the recognition, at least with the current version of the system. You should be aware that the sulcal patterns have been learned from a group of only 16 brains, most of them between 20 and 30 years old, and worst of all french. Our system is still weak in terms of generalization power... I do not mean that manual correction is mandatory. If you have enough brains, you can get interesting effects (we have performed a lot of such studies in Orsay, to be published...), but when you are at the beginning of a study, you have check everything until you reach the point where you are sure that the parameters chosen for the pipeline and the quality of your data lead to reasonable results.

Can you see simple images with Anatomist?
Manik
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Post by Manik »

Could you explain what happens exactly when you try to look at a graph ? Does it happen when you load the graph in Anatomist ? When you put it in a window to display it ?
With an old version of nvidia display driver I once had a lock-up of my computer, which happened with any image displayed in Anatomist when I was moving the view (rotation), but recently I never had that kind of problem.
Manik Bhattacharjee
INSERM U836
cyril
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linux crash report

Post by cyril »

Thanks for the reply ..

ok I agree with JF that checking the labelling will be better .. and French brain are ok (je ne m'en plains pas)

the crash happens this way: I load the automatic recognition, once it is done, look at the output graph - this loads the graph in anatomist (no prob) and open the visualisation window - then I click on some part of the brain and .. crash .. kernel error (sounds bad!!) Next, as Linux is clever (more than Windows) it closes all windows. And yes Manik I run a nvidia but very recent .. (but if u know a bug I take it)

thanks in advance
cyril
cyril
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Post by cyril »

let me add smthg: it mainly crashes with object scaling, i.e. zoom, rotation, or resize the window .. this kind of manipulations
Manik
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Post by Manik »

I am not sure, but it looks like an OpenGL problem, and the "kernel error" is consistent with this, because the nvidia driver loads itself as a kernel module. You may have more information about what happened with the last lines of "dmesg" output in a terminal just after the crash, or in /var/log/Xorg.0.log

When searching in google, I found interesting problems with opengl :
http://www.google.fr/search?q=nvidia+op ... sh&start=0

If other openGL programs do crash on your computer, Anatomist has probably nothing to do with the problem.
A very slow solution would be to remove nvidia drivers and using the standard driver (nv) with the software emulation of OpenGL (MESA library), until nvidia fix the problem - it may be related to your card being a very recent model badly supported by their driver.
Manik Bhattacharjee
INSERM U836
klargenf
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Post by klargenf »

well, i should say that i just begin to use Linux for several days and consequently i know nothing about that. For the moment i can just tell you that i was told to work on a newly bought PC with a ATI-RadeonX600 video card and a Mandrivea Linux 2006 installed on it. I can't visualize any sample image downloaded on you site. If you would like to give some helps to a well beginer who works at CERMEP in Lyon and if you would like to make you soft a satisfying one, please find me an acceptable and feasible solution for our case.

Très Cordialement.
Manik
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Post by Manik »

I was trying to help but I am not a developper of Brainvisa, and nobody here is forced to help you. If you want some help, you have to describe precisely your problem and not just "it does not work".
Those working on Brainvisa and Anatomist are providing the software freely but you are not entitled to free support. Please keep this in mind when you write messages on this board.
You must install the OpenGL drivers for linux for your ATI card, and even with those it may not work as ATI support on linux is poor.
Anatomist needs OpenGL libraries, and if they do not work properly, nothing can be displayed. I know that most people use NVidia video cards with nvidia driver, and some people have successfuly used ATI cards with their drivers.
Depending on the Mandriva linux version (download version/powerpack....) you may have those drivers in your distribution or not.
If you have no idea how to install them, search on the web or ask someone who has some knowledge about linux.
Cordialement,
Manik Bhattacharjee
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riviere
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Post by riviere »

Hi,
ATI (just like Nvidia) drivers are not part of standard free linux distributions. They are in mandriva non-free version (I don't remember its name).
But you can get these drivers for linux on ATI website. We have no experience with them: all our machines have nvidia cards because ATI drivers used to be bogus (this is clearly explained on brainvisa website), however some people have reported them to work now. So, just try them, and tell us...
Denis
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