BrainVISA

Hi, a colleague trying to segment a lesion on an T1 MRI (nifti file) using Anatomist ROI module and exporting the resulting mask as nifti was unable to view it in SPM alongside the T1 with a synchronized cursor. It seems the problem is that exporting a ROI as a mask does not keep the geometrical tra...

Sorry, the test file was too simple, not creating Anatomist nor a Qt App...

Hi, trying to use anatomist.cpp results in a segfault, using a new brainvisa-4.2.1 package and a simple test file : # -*- coding: utf-8 -*- import anatomist.direct.api as anatomist class TObj ( anatomist.cpp.TextObject ): def __init__( self, message='', pos=[0,0,0] ): anatomist.cpp.TextObject.__init...

Thanks. For the first question, I am wondering how I can specify the referential of the TextObject, as I found little documentation about it : - there is text label with a position - there is a line "polygon" to link the label to the position of interest. The object that I want to label wi...

Hi, is there a way to have labels displayed in Anatomist in a 3D window ? The sulcus tooltip that displays the name of a graph element is ok, but it is linked to the mouse cursor and only one is displayed at any one time. I would like to display a label linked to a fixed point of a mesh. For example...

Thanks !
I hope this will be also useful to others because I will keep KDE anyway !

I got the same problem on Ubuntu 12.04 64bits with Brainvisa 4.2.1 64bits. Removing libcairo* from Brainvisa did not work (it even caused X to use 100% CPU, I had to go to the console to kill python to go back to a usable mouse/screen). I installed KDE and switched the default Ubuntu session to KDE/...

Hi, I just installed BrainVisa 4.1.1 and Anatomist on a Windows 7 PC with a NVidia Quadro 600 graphics card. After installing the latest NVidia driver, each time a window is opened in Anatomist, the window is blank and in the terminal, there the following error : "unrecognized OpenGL version&qu...

Hi,

you can ask Marie directly about her software, I know she is still improving her program and the brainvisa processes.
I will send you her address through a private message,

To solve the problem, there may be alternatives in the pipeline 2005 elements, but you need to ask Jean-François Mangin how to use them with your data (you need to use locks to prevent Ana Do All from destroying the 2005 output files). I also think that you need all Ana Do All processes to get the s...

About the VIP Warning, when I see it, I usually have a bad result, but sometimes it is ok anyway, I am not sure what this means. For the filenames, you should create and use a BrainVisa database : create an empty directory, and in Brainvisa menu Preferences/databases you should add a database in thi...

In the error message there is this line : Sorry, ComputeVolumeHisto is only implemented for S16BIT volume It seems you have to convert your image to a signed 16bit image. In Brainvisa, you can convert your image using "converters/automatic/Aims Converter" You should open your image with it...

Hi, it seems that BrainVISA just calls brainvisa/brainvisa after setting a lot of environment variables. The variables you used are not enough to have the proper environment for brainvisa/brainvisa. Why do you want to use brainvisa/brainvisa, as the standard way to use Brainvisa is to use BrainVISA ...

If you want to read a .trm file in matlab, you can use m = textread('file.trm') The .mat format can contain anything (rotation matrix + vector, quaternion), so it is impossible to understand what kind of .mat you want to get. The .trm format, as far as I can remember is Tx Ty Tz R11 R12 R13 R21 R22 ...

If you like to try things out and if you don't mind spending some time on this, you can probably compile the whole pack yourself on your system, but you will need to install a number of libraries and I am not sure it will work in the end... If you still want to try, download the source package (same...