Visualising edges as streamlines / streamtubes

connectomics

#1

Dear all,
I receive an empty track image when trying to visualise the exemplar track file in the connectome toolbar with edge visualisation - geometry - streamtubes.
Streamlines is working though. What am I missing?

(http://mrtrix.readthedocs.io/en/latest/quantitative_structural_connectivity/connectome_tool.html?highlight=streamtubes)

Thank you ever so much!
Best, Lucius


Connectome node mesh visualisation problem
#2

Hi Lucius,

I’m unable to reproduce this issue. I would be curious to know whether you also suffer from the issue of visualising nodes as meshes as reported elsewhere on the forum: perhaps there’s been some update to a video driver or whatnot, which has invalidated an assumption I’ve made when writing my GUI / GLSL code, and hence multiple issues are cropping up in this context.

Rob


#3

Dear Rob,

visualising nodes as meshes is perfectly feasible (unsmoothed and smoothed meshes).
I noticed that when I directly want to visualise as streamtubes (without visualising first as streamlines), mrview crashes (on two different macbook pro’s). Changing from streamlines to streamtubes then results in above posted empty image. I’ll check on a different computer next week.

Lucius


#4

I noticed that when I directly want to visualise as streamtubes (without visualising first as streamlines), mrview crashes (on two different macbook pro’s).

That’s interesting; I made sure to test precisely that use case on my own system in debug mode, and it didn’t have any issue.


#5

I just tested the crashing again, this time it didn’t happen :roll_eyes: . But the streamtubes are still not showing up.
I’ll test it again next week on a power mac and communicate it here.


#6

I tested it on the other computer. First, the mesh structures weren’t showing. This solved it (changing the system language from german to US english): Connectome node mesh visualisation problem.

Unfortunately, changing from streamlines to streamtubes still results in no streams at all.


#7

Hi Lucius,

Thanks for the feedback. Given the relevant mechanisms of node mesh and edge streamtube visualisation, it doesn’t surprise me that the solution for the former does not additionally solve the latter: The streamtube geometries are generated entirely within mrview's working memory at execution time, and so localisation cannot logically have an effect. So my “grouping” of these two issues seems to have turned out to be a red herring.

I’ve not been able to reproduce this issue, but given your description and @albertofpena’s comment in the other thread here, I’m thinking it may be a problem specific to Macs. If you’re able to get mrview running with a debugger, that could be very insightful. There’s also now a dedicated GitHub issue for this specific problem, given it appears to be entirely separate to the node mesh visualisation bug.

Rob


#8

Dear Rob,

I just posted the debugger error output at the GitHub issue page.
Hope it helps…

Lucius


Connectome node mesh visualisation problem