BrainVISA

Hi, Working with un-normalized EPI volumes, I need to convert my voxels/matrix coordinates into the mm anatomist coordinates. To be more precise, I'm talking of the mm coordinates that get displaied in anatomist after you just open the nifti file (before assigning any referential to the image/window...

Hi everybody, We have a set of MR images acquired with an Inversion Recovery sequence (see attached example)... Before I try and mess around with them randomly, I was wondering whether anybody has already processed this kind of images, and whether you'd have any advice on how to pre-process them in ...

little update...

if we do this before launching anatomist
export LIBGL_ALWAYS_INDIRECT=y
(which is a trick we had to use in some cases with past versions)
then we switch to case 1 of your windows post (display windows are all white)

sylvain

Hi Denis, We found another case in which we found problem 2 (the one described in your windows post): when running anatomist remotely on a unix server (running debian)... We have a centralized unix server on which people in our lab log on to (from unix or windows desktops, through a standard 'ssh -X...

excellent, looking forward to it so that I can try to use it in my code!!

if you want me to beta-test, let me know!

cheers,

sylvain

Hi all! I use AimsSubVolume on a T1 image, and the resulting cropped image seems to have a problem: when I display it in anatomist, it looks as it is "cut" (see image below) cropped.png and anatomist gives me the following message: Warning: storage_to_memory transformation in NIFTI1 file s...

It's not a Brainvisa-related answer, but well, it might help: the "New Segment" procedure available in SPM8 produces a segmentation into 8 different classes, one of them being "skull"... The segmented skull probability map could be a good starting point to answer your question...

riviere wrote: - Lowering of disabling the decimation/smoothing may help, inversely. I am not sure if completely disabling it would guarantee a good behaviour or not - I have not tried, to be true.

OK, I'll try to look into this... Thanks Denis!

Hello Denis, thanks for looking at the data... It's not really the answer I was hoping for, but I understand the situation ;) Here are two extra ideas/questions that might help me at this point: - is there a way to "fix" a mesh with intersecting polygons? some resampling could do, for exam...

Hi Denis,
I just tried it again to check the CPU usage, and it did stay at 100% during those several minutes, so it seems that it's actually computing something...
Sylvain

...hmmmmmmmmm, actually, after having killed the process the first times it happened, I didn't kill it the last time... and a few minutes later, it unfreezed and said: 12126 points processed 5286 vertices / 1762 polygons in planar mesh so it must have been computing something... the result is totall...

Hi Dominique, thanks, that solved it ;) I'm a bit lost in the definition of the slice_ or view_ quaternions of the camera command, but I'm working on it... I found another problem, with the sliceParams command of my cut mesh fusion this time... I can define a sagital ( plane=[1, 0, 0, -48] ) or coro...

Hi Denis, thanks for your answer! Hi Sylvain, You can use the SliceParams command to set the cut mesh plane. You may specify the plane either using a quaternion (rotation from the axial plane), or more simply by giving the plane equation coefficients: a.execute( 'SliceParams', objects=[cutMeshFusion...

Hi all, I'm trying to script some little things, and I need some help to go a bit further... For now, my script aims at opening a T1, a mesh, do a CutMesh fusion. I'd like to control, through my script, the orientation of the cutting plane in that fusion (by default it seems to be axial): first, I'd...

Hi Denis, thanks for your answer, that was indeed a problem of version of libreadline! The first line of your suggested test ('import readline') failed, telling me that libreadline.so.5 was not found... And indeed, only libreadline6 was installed on the system... So I installed libreadline5 and ever...