Connectome node mesh visualisation problem


#1

Hi all,

I’m having some trouble with the option "Node visualisation” - “Geometry” - ‘Mesh’. When I try to visualize nodes as meshes the surfaces are not correctly displayed. Instead of the mesh what I can see is a “slice” as you can see in the attached image:

The .obj file was generated using label2mesh command and it seems to be ok when I load it in MATLAB.

Thanks.


#2

Hi Alberto,

It’s difficult to see exactly what’s gone wrong from a single screenshot, so I might need to get the data from you to have a look; preferably the node image, the .obj file and the connectome matrix, everything I would need to reproduce this exactly.

It is however worth clarifying / checking one thing: If you use label2mesh (particularly if you use the -blocky option), and don’t subsequently use meshfilter smooth, then each node will have a lot of polygons with identical normals, which correspondingly appear as homogeneous “blobs” of colour in the screen projection due to the relative simplicity of the lighting effects used (e.g. no ambient occlusion). It’s possible that the nodes are in fact all 3D blobs, they just don’t look as such from a static screenshot; simply rotating the camera around should answer this question. This effect is accentuated if your camera position is on the opposite side to the light source, since the diffuse & specular light components will be uniform for most polygons; try rotating the azimuth of the light source.

Some nodes also look like the centre of mass (where the edge lines converge) is outside the surface representation, which would be problematic if that is indeed the case.

Rob


#3

I’ve emailed you the data I’m using. I’ve tried the mesh with and without the filter and the results are very similar, a thin slice or plane. Rotating the azimuth of the light source didn’t fix the issue.

The version of MRView I’m running is 3.0_RC2-132-ge25f7c6d on a Debian machine with NVidia drivers.

I also attach some new screenshots with different angle positions.



Thank you for the answer.

Alberto


#4

Hi Alberto,

Thanks for forwarding the data. Here’s what they look like on my system (deliberately recreating your original configuration as much as possible):

As you can see, the data are in fact perfectly fine. This would suggest that there’s something going wrong specifically with the visualisation on your system. Therefore can you provide:

  • What OS and version you’re running on

  • The output of mrview -version

  • The contents of “OpenGL information” accessed via the blue “i” icon in the top-right corner of mrview

  • Whether or not you can produce / have produced any other kind of visual artifact using any other functionalities within mrview

You could also try viewing the same data on another machine if possible.

Cheers
Rob


#5

I’m running on Debian Testing (buster) with kernel 4.15.0-2-amd64. My output of mrview -version is:

== mrview 3.0_RC2-132-ge25f7c6d ==
64 bit release version, built Apr 10 2018, using Eigen 3.2.10

Here is a screenshot of what I have in the OpenGL information window:
imagen

I don’t remember any previous visual artifact with mrview. I’ve done visualization with spheres and cubes. I’ve also plotted ODFs without a problem.

I’ve tried viewing the data I sent you in a Ubuntu 16.04 with Intel Graphics and in my laptop with Debian Testing with Intel Graphics too and I have the same problem in all of them.

I’ve also tried to run mrview with -debug flag, but I didn’t see any relevant message. If you want me to try something else, please tell me.

Alberto.