Hi,

I am running BrainNet Viewer (versions 1.43 and 1.6) on Ubuntu 16.04. I can properly create and display a connectome. However, I am having great difficulty saving the resulting mage. Both the GUI and command-line "save" functions either cause my Matlab to crash, or (in the rare even it actually creates a file) the image is not rendered properly. I have successfully executed these commands on other Debian, Ubuntu and CentOS releases, so I have no clue what the problem is. 

Any suggestions/advice would be appreciated. 

Thanks.

- Archana

Hi Archana, 

Thanks for this feedback, I have never met this issue before. We tested BrainNet Viewer with Matlab 2015b on Ubuntu 16.04, and it works well. Could you please check the version and related functions of matlab on that machine? The function "print" of matlab is used to save images in BrainNet Viewer. 

Best,

Mingrui

Dear Mingrui,

Thank you for the feedback. I was initially using Matlab 2012b and not able to save my images. I have switched to Matlab 2015b, and while the save operation works, I have run into another issue. Specifically, the networks render differently in 2012b and 2015b. I am attaching a screenshot. The figure on the left was generated using Matlab 2015b and shows visible occlusion of the brain connections (the occlusion is worse in the saggital and coronal views). The figure on the right was generated using Matlab 2012b and is the image I would like. I have played around with the surface transparency, but I am not able to restore the edges with Matlab 2015b.

Have you come across this issue before? If so, do you know if there is a workaround?

Thanks.

- Archana

Hi Archana, 

This issue doesn't occur on my test machine (a virtual machine Ubuntu 16.04 and matlab 2015b, please see the attached figure). However, I've met this before. Several factors may have effect on the rendering, including the type of graphic card, the OS, and the version of matlab. It is too complex to examine their exact relationships. I think one thing you can try is to switch the render from opengl to zbuffer in the global section of the option panel. It sometimes fixes some unexpected issues. 

Best,
Mingrui

Dear Mingrui and Archana,

Thank you for pointing out this issue.
I ran into the same problem: rendering the images is fine, but when I try to save it, Matlab crashes (i.e., gets stuck being busy forever).
The option to switch from opengl to zbuffer allows me to save the images, but the problem is that the brain is not transparent anymore so the connections cannot be seen when using zbuffer.

I would be happy about any suggestions to resolve this!
Best,
Andreas

Hi Andreas,


In my case, I could save the images using Matlab 2015b, but the brains were not rendered correctly due to a visualization change after version 2014b. Matlab 2012b produced a nice brain image, but I could not save them using any of the BrainNet Viewer commands. I ended up taking screenshots of the BrainNet Viewer window using the import function (part of ImageMagick). The images look fine in my paper.

Hope this helps.

- Archana

Hi Archana,

Thanks for your feedback! Indeed, screenshots did the job.

Best,
Andreas