BrainVISA

Zahir is right, but there is also a more easy way to initialize the drawing part for tracking: in BrainVisa, the "starting points" parameter is the filename to the ROI, there is a "pen" button which directly puts anatomist into ROI drawing mode, with a session and some (empty) re...

Just a precision: the command to merge meshes is AimsZCat
Denis

What do you call a "3D whole brain image" ? For me a T1 MRI is a 3D whole brain image. Maybe you mean a mesh of the brain ? This is one of the outputs of the segmentation tools of BrainVisa, so yes, sure, BrainVisa+Anatomist can display such things. But I think I don't really understand yo...

Are you sure you get exactly the same error message as before ? I guess you don't, for several reasons: - your last message has windows filenames (D:\...) whereas your previous one had unix filenames (/home2/...) so you appear to have changed system between the two messages, this doesn't help to und...

Hi Christophe, Right now there is no module in Anatomist to directly draw lines or arrows for electrodes, but there are a few other things that you can use as a starting point (in fact I'm not sure if you want to be able to manually draw electrodes or display the position of calculated sources): - t...

The path to your voronoi template seems really strange: /home2/local/Panabase/demo/talairach/... It seems to take it in your personal database, whereas it should be in <installation_dir>/SHFJ_pack-stable-2.3.x/share/shfj/hemitemplate/closedvoronoi.ima Did you specify it by hand or something ? The te...

Hi, AimsVoiStat should find its libraries (otherwise there's a big problem in our binary package but in this case almost nothing would work in BrainVisa and I guess other people would have already complained). Are you sure you have correctly run the environment variables script ? - you must use the ...

Hi Zahir, 1. The current stable release of Anatomist only allows to choose a brush shape (point, disc, sphere) with a size in voxels. If you are using images with anisotropic voxels, it will probably be difficult to precisely obtain the surface you want. The development version allows to choose the ...

Have you made sure you saved the starting point regions ? (you just have to select "save" in the "session" menu of the ROI box in Anatomist, or hit ctrl-S). I don't use the tracking module every day (Yann is on holiday and will be back in about 3 weeks) but as far as I see when I...

Hi Pascal, You can convert SPM normalization matrixes (only the affine part) to transformations readable by anatomist using the SPMtransformToAims process ofd BrainVisa (found in converters). Then you can load both images in Anatomist (and/or meshes), assign a referential to objects in the normalize...

No, it's still here.
Did you check it's compiled (you should find a libroibase.so in the lib directory of anatomist) ?
If not, are you sure you have qwt installed ?

Denis

Hi Manik, Two little things: 1. It seems that providing RGBA colors in hierarchies just work fine, I just tried it and obtained some transparency in both stable and development versions. Doesn't it work for you ? 2. I've added in anatomist (development branch) the possibility to provide materials in...

Hi,

Can you please send a full log file to the support email address using the "bug report" option of BrainVisa ? Did you indicate a lesion mask ?

Denis

Our images here are acquired in radiological convention. So the default parameters consider images to be in radiological mode. But if you know your data are in neurological convention, you can just change the value of the parameter in brainvisa (there is no way to guess the orientaiton of SPM images...

Hi Manik, The axial orientation in Anatomist corresponds to volumes being seen from the bottom, so when a clipping plane is activated, the bottom part is clipped and the top is visible. You can change the orientation of the clipping plane by changing the orientation of the volume slice plane: rotati...