BrainVISA

Well, do you need that for practical reasons? in which case you can just merge the two meshes (There should be a AimsMeshCat somewhere). If you really want a continuous mesh, I am a bit surprised. The cortex, indeed, is interrupted at the level of corpus callosum, so there is no real reason to build...

The registration toolbox of brainVISA is not developped yet. Various people are thinking about it. Therefore, there are some registration tools behind but not with a clear interface. The most general way to align images is the AimsMIRegister commandline, which should yield a transformation file. Thi...

Well, I think what happened is that the command as been triggered without the template to guide the split. Normally, thie template filename is filled in automatically by brainVISA. It is hidden somewhere in brainVISA dependencies. If you removed it manually, it seems a local setting of the SHFJ is t...

Basically, the process aiming at splitting the two hemispheres and the cerebellum uses a threshold to get a first raw definition of white matter. This threshold is applied to the tissue inside the brain mask. It is defined from the estimation of grey and white matter average performed by the histogr...

I apologize for the lack of documentation about all this. Our ROI-module is improving little by little :wink: An increasing number of people are using the developement version in the lab, so we hope to release a better version this winter. For the moment, you may obtain the simple statistics you are...

I am not sure I catch exactly the question, you should be able to import a dicom file directly using the importation process of brainVISA.
Otherwise, the AimsFileConvert command does all the conversion jobs.

If you just want to obtain simple morphometric descriptors (size and length of the sulci, location of extremities and center of mass...), there is a brainVISA process for this in anatomy/morphometry. This process creates ASCII file for a list of brains with all the descriptors (see its doc). Note th...

There is no limit to the number of objects that can share a window. To add some object to your window including fibers, you can just drag and drop it, taking it from Anatomist control window. Drop it either on the window with fibers or on its icon inside control window. You can also use the reverse ...

I think there is a misunderstanding somewhere, most of the time the lesion mask line is not filled (it is not a mandatory parameter at all). This is supposed to be used in case of a big lesion inside the brain disturbing the segmentation process. In such cases, the lesion has to be drawn manually or...

Yes, the sulcus recognition system is still a very young one :wink: , It learned anatomy from only 16 brains. Hence, it is still disturbed by some new brains. Maybe for instance because it knows only french brains :D We spent most of our energy during the last years reaching the current state of our...

Hi, Go into the preference of brainVISA, select the expert user level. Then additional brainVISA functionalities will appear, for instance the possibility to create volumes of labels corresponding to the sulci in anatomy/morphometry. For the projection of the sulci on the cortical surface and the co...

Well, you should manage to do what you want without going into the graph format. There is a brainVISA treatment (in anatomy/morphometry I think) which allows you to create images of the sulci, where they are represented by voxels. I think this is the simplest entry point. Sulci, indeed, can be made ...

I do not know which version of datamind you use Olivier,
but anyway, if you select n sulci, you should get n plots
in the figure?

A related question. Say I want to depict certain information (cortical thickness) on the inflated map. I do have the thickness value for each node in the "un-inflated" state - how would I go about depicting them on "inflated" state. Do you save the deformation information anywhe...

I strongly advise everybody to be reasonably patient with the processes that are still in advanced user levels. It means they are still under test in the lab developping them. We do not completely hide them because this testing period can be performed across several betasites. Playing with them else...