BrainVISA

Hi, after correcting the mask, you must launch "Anatomy --> T1 pipeline 2004 --> validation --> Validation_3 Brain Mask from T1 MRI" in Brainvisa, choose your brain mask, and choose validation "lock", then run the process. Now the brainmask is locked, so it won't be overwritten.

Je crois me souvenir que c'est dû à un problème des drivers 3D (OpenGL)de la carte graphique qui renvoie une valeur aberrante à Anatomist quand on clique dans une fenetre. Je crois que c"etait avec une carte video ATI et des drivers assez anciens. English version (as this forum is supposed to b...

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...

Hi, I do not know if someone is working on this kind of process, but I can tell you that your project is realistic and feasible. I think you could convert your data to a format like the graph format of anatomist (.arg file with associated data). I am not an expert about this, but I think you can put...

I do not have a Fedora 5 distribution, so I don't know where the C library (libc) is supposed to be.
It seems that the setup.sh does not find it.
In my distribution it is in /lib/libc.so.6
You can check its path with :
/sbin/ldconfig -v | grep libc.so

The problem is due to OpenGL driver problems on your computer. You should update your driver, probably on the following page, but I am not sure it will solve everything : http://www.intel.com/support/graphics/i ... 011906.htm

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 cras...

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 Anat...

If you have installed the nvidia driver, you can check if it works using glxgears (if it is installed on your computer). The speed is very high if the driver works : [manik@pclx8 testData]$ glxgears 28771 frames in 5.0 seconds = 5754.200 FPS Could you give more information about what is installed on...

I had a lot of problems using an external drive for the Brainvisa database, but it was because it was formatted for windows (fat32 filesystem) and not for linux. As long as yours is ext2/ext3/reiserfs it should not be a problem. Or maybe there is a per-drive limit as well ? How do you mount your ext...

This error is reported by python because the maximum number of open files was reached. This is really strange, as it is usually a very large number. To see the current value of the maximum : cat /proc/sys/fs/file-max (you may need to be root) The value returned is 102530 on my computer, how much is ...

If you want to change the contrast on your screen to view the brain better - I do not know if you just want to see the brain shift or if you really need to segment the brain and launch automatic processes - you can try to change the contrast of the image in Anatomist. When your image is open in Anat...

There is also a Brainvisa version of Marie Chupin's work (I did it with her), but I am not sure about the distribution of this package. You can ask her directly by using the private messaging function on this forum, for the user marie chupin. Just click on "pm" on this page : http://brainv...

To use the 2005 bias correction, you should run the bias correction process of 2005, then lock it to prevent the 2004 pipeline from destroying it. To lock it, just use the process in Anatomy/T1 Pipeline 2004/validation/Validation_1 Bias Correction from T1 MRI with the validation parameter set to &qu...

This also happened to me a few times.
There seems to be some bugs in DICOM importation, so I use other software to convert the "bad" dicom images to Analyze or GIS format.