BrainVISA

Hi, as far as I can tell, almost all the processes you used are designed to work with T1 MRI images, not with CT-scanner images, and probably won't work with them (I will let the designers of these processes answer if it can work). For your first point, I do not quite understand why you exported you...

Usually, you have a DICOM directory for each acquisition (one for T1, one for T2). Each directory contains one file per slice image. You should be able to open an MRI sequence in Anatomist by opening one of those files in Anatomist : just load Anatomist and click on the "Open" icon, choose...

To see 2 perpendicular slices of the same MRI in Anatomist, load the MRI, select it and click on the "fusion" icon. It will create a second object. If you put both objects in a 3D window you will see them (click on the orientation icons under the 3D window menu to have 2 perpendicular plan...

Hi, I can also say that Brainvisa/Anatomist works on an Acer laptop with ATI graphics card using the Kaella Linux distribution version 2.0 (which is a french version of Knoppix live CD). I suppose that it uses only the open source drivers provided with X.org, and MESA as the OpenGL library (which is...

You should use the process in anatomy --> shfj-low-level --> VipBiasCorrection
You must be in the advanced level (preferences).
Or you should run the whole anatomy pipeline in anatomy --> pipeline using the documentation on Brainvisa website.

As far as I know, it is :
tx ty tz
m11 m12 m13
m21 m22 m23
m31 m32 m33

with t a translation vector and M a rotation/scaling matrix.
Thus, if you have a point X it will become t+m*x

Hi, if you want to use the transformation file in a BrainVisa process, you can do something like this : a = anatomist() mri = a.loadObject("myMRI.ima") # Default referential = a.centralReferential window = a.createWindow("3D") talairachRef = window.assignNewReferential() a.loadTr...

Using the command line tools you have AimsComposeTransformation which can compose .trm files. I don't know if there is a BrainVisa process available to do that.

Hi,

I wrote some time ago a very small documentation (in french) for development in BrainVisa.
Yann, I will send it to you, if you consider it is correct, you can put it somewhere on the website.
I will try to translate it to english as soon as possible.

If you want to have only one mesh, you can use in a terminal AimsZCat -o oneMesh.mesh -i sulci*.mesh if all your meshes' names begin with "sulci" If you want to create a graph (what is done when you use "ana compute a fold graph"), you can use AimsMeshes2Graph -o graph.arg -i sul...

Hi,

if you do such a process, could you make one that can be used to import any dicom image as a GIS image ? Because I have some DICOM images (3D-MOTSA sequences) that can be imported with medcon but not by BrainVisa (I gave you one of those a few month ago).

Thank you very much !

Hi, I had forgotten about this problem, but yesterday, I tried to enter AC-PC points in Brainvisa/Anatomist, and I found a way to freeze BrainVisa with the same error as before. - Open a "Enter AC-PC" process - click on the Anatomist icon to enter AC - in the MRI window, right click, "...

Hello,

is this a DICOM image ?
If so, I had problems with some dicom images. You should try to convert it to GIS format or another format known to BrainVisa (SPM, for example) using another tool.

Hi all, I tried to load 4 graphs objects (G1, G2, G3, G4) in Anatomist and two hierarchies (H1 and H2). H1 and H2 have at least one name in common, which might explain the problem I have. I would like G1 and G2 to have the colors defined in H1, and the same for G3 and G4 with H2. I can select the ri...