tool box

Questions about BrainVisa usage and installation

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delpach
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Joined: Mon Jul 17, 2006 3:00 pm

tool box

Post by delpach »

I would like to manipulate the masks used to generate the mesh during the segmentation process, I've seen there is a toolbox for that purpose. I understood how works MorphoMath but I don't understand the rest and especially ConnectivityThreshold. Is there any documentations or informattion for that tool box somebody may provide me.

Thanks.
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Jean-Francois Mangin
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Post by Jean-Francois Mangin »

I am not the sure the toolbox inside brainVISA is really operational, only a few command lines have been provided an interface. However, you have access to all our tools using the command lines.
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Yann Cointepas
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Post by Yann Cointepas »

If you describe more precisely what you want to do with the mask someone could eventualy give you hints on how to do it.
delpach
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Joined: Mon Jul 17, 2006 3:00 pm

Post by delpach »

The low quality IRMs that I got engendered bad segmentations, that why I would like to work on the masks.
Thanks a lot.
SylvainT
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Post by SylvainT »

delpach wrote:work on the masks.
I don't think this is detailed enough for yann to be able to help you ;)
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Jean-Francois Mangin
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Post by Jean-Francois Mangin »

Did you notice you can do some manual correction if you click
on the pen icone near the mask?
However, before doing any painful manual work, you should better
try alternative of the segmentation process (in the correction
directory of 2004 package).
Personally, I did not do manual correction for a while, because
it is often misleading. You solve the problem at the level of
the mask but new problems occur further. Of course,
if you just wanna access a 3D rendering, it may be sufficient.
denghien
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Post by denghien »

Hi,

The "ConnectivityThreshold" panel works. It's a kind of manual segmentation by using of low and high threshold.
If yo are french, so you can read the manual, which is available on the http://brainvisa.info/downloadpage.html in the 'Example data' section in the following package: 'demo_data'.

Otherwise, in few words, to use the ConnectivityThreshold:
1- Create a session and region for your image
2- Click on 'Active Threshold Preview'
3- Select a region with the "Low Level" and "High Level". The blue region is the selected region.
4- To store this selection into a region, click on the level icon on the image windows (the icon with blue wave). Then, click on the image the zone what you want. The blue zone becomes purple. All connected voxels are selected.

Note that you can select a 2D or 3D region. And you can directly export this region into a mask with 'Region -> Export as mask'.


Isa
salemhannoun
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Joined: Tue Mar 27, 2007 2:08 pm
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²bonjour

Post by salemhannoun »

bonjour, je suis entrain de travailler sur la diffusion, j'essaye de faire des roi sur l'image IRM de T1et puis de les transferer sur la diffusion pour etudier la FA et la MD, mais le programme que j'utilise MedINRIA ne prend pas les roi, il dit qu'ils n'ont pas les meme parametre.
alors j'ai utiliser brainvisa pour faire un superposer les 2 images. j'ai utiliser Registration Mutual Information Method pour faire cela. il m'a donnée 2 matrices que j'ai utilisé dans anatomist pour fusionner les 2 images de diffusion et de T1 et ca a tres bien marcher. mais moi je veux maintenant transformer seulement la T1 pour pouvoir dessiner les ROI et les transferer directement sur la diffusion sur MedINRIA. alors pour appliquer la transformation a la T1, j'ai utilisé Resampling dans la Toolbox, la transformation se fait en utilisant les matrices calculés pour la fusion dans anatomist. mais la quand je fais les ROI et je les tranfer sur la diffusion, il ne sont pas au meme endroit, exemple: j'ai fais un ROI du corps calleux sur la T1, sur la diffusion on le voit mais soit audessus, soit au dessous, soit a droite ou a gauche mais jamais superposé.
je ne sais plus quoi faire pour les superpose roi et diffusion ensemble. j'ai presque tous essayer en changant la matrice (soit ref to test soit test to ref)
s'il vous plait si vous avez une solution je serai tres reconnaissant.
denghien
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Post by denghien »

Hi,

For information, the forum is english and each request is independent by using a new subject. So I created a new subject, please see

http://brainvisa.info/forum/viewtopic.php?p=3531#3531

Isa
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Jean-Francois Mangin
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Post by Jean-Francois Mangin »

Maybe your life would be simpler doing everything with the same toolbox...
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