BrainVISA

thanks, Denis!

OK, I understood... The ACPC coordinates are "imported" from freesurfer, so we only have to say that the image is NOT normalized to "Prepare Subject for Anatomical Pipeline". One question though: that gives some sort of warning because the "left hemisphere point" is not...

Hi, I'm trying to run Morphologist with the new BV 4.4 (to then run the Cortical Surface Toolbox's Hiphop process) on some data that has been processed with Freesurfer. I ran the "Import from Freesurfer to T1 Pipeline" successfully... And now, I'm wondering which option I'm supposed to cho...

Hi,

I'm wondering whether there's an option to launch a .bvproc from the command line (i.e without having to launch the brainvisa interface)... I've looked at the options (BrainVISA --help) but I didn't see anything to do this...

Thanks,

Sylvain

Hi, I've ran the 'Freesurfer / Brainvisa full pipeline', but I have a problem with the resulting meshes... I'm just trying to visualize the results in anatomist, by overlapping a white mesh (any of lh.white.gii, lh.r.white.gii, lh.r.aims.white.gii) on the T1 (001.nii or T1.nii), but it just does not...

Hello!

I'm wondering whether it's possible to tell brainvisa not to create and store the .brainvisa directory in $HOME, but somewhere else...

Cheers,

Sylvain

hmmmmmmmm, sorry, I posted too early and hadn't realized it was the same kind of problem as the one reported here (and other threads):
http://brainvisa.info/forum/viewtopic.php?f=6&t=1573

I moved away the *cairo* files from the brainvisa/lib directory, and it works for me now!

Hi all, I'm trying to use surfpaint to define manually a ROI on a mesh... It works fine (I draw a closed path with the geodesic path tool, fill it, use the magic wand to select all the nodes within this region, then fill it)... But when I click the "Save texture" tool, it crashes (anatomis...

Thanks Denis, that works!!

by curiosity, what's the difference between
and
And are there circumstances when one should use one or the other?

another question... I'm doing something like... from soma import aims import anatomist.direct.api as anatomist a = anatomist.Anatomist() mesh = aims.SurfaceGenerator.sphere(aims.Point3df(0,0,0), 1, 500) asphere = a.toAObject(mesh) and then I need to delete the asphere object from anatomist (coz in f...

Thanks Denis for your help! That does everything I need! And I didn't know about some of the links you mentioned, so there's tons of info in there that I'm sure will be useful ;) Just one detail: this did not work... a.camera( force_redraw=True ) ...but I just had to include the 'force_redraw=True' ...

Hi there, I have a pyanatomist script which helps me do systematic visualization of objects I'm creating... I have a lot of them (several hundreds), and I'd like to be save a jpg for each of them within my script, as seen from a Fixed point of view... In details, I need to do three operations that I...

Thanks Dominique, moving the BrainVisa installation dir somewhere else makes it work! And actually, since we always install BrainVisa in the same place (system-wide in /usr/local) on a server for a bunch of users in our lab, we'd seen this kind of problems several times (when launching different app...

Hi all, I'm trying to use the FSL normalization within morphologist... (having to process a lot of subjects, I want to avoid clicking on AC / PC every time) I'm on debian squeeze with BV 4.1.1, and the neurodebian version of fsl (the one with all executables starting with the fsl-4.1 prefix)... I ge...

Hello Denis, Yes, that was my question! I was trying very complicated stuff, but the answer was indeed quite simple (Olivier C. had helped since; that was also related to the graph questions he'd sent you coz I'm trying to do some graph visualization... I wanted to mention it on the forum but I forg...