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Dear colleagues,
Once again my best wishes and sincere prayers to you all and thank you for your cooperation.
Just have a question regarding mri colin segmentation data accompanying brain stimulator.
As I have a problem with viewscene module on linux, I used octave to read the file and export it to vtk format. When I opened it using paraview, I can see there are a 7 labels: this is my guess but I am not sure it is right:
0 is bounding box
1 scalp
2,3,4 skull
5 CSF
6 grey matter
7 white matter
am I correct?


On 21 ماي, 2015 م 07:17, Dan White wrote:

It's the ViewScene module specifically. The GUI should work with a blank network, and you should be able to use every other module provided to read in data, process, and write out matrices and fields. I believe all networks in the BrainStim package include a ViewScene in them, so you'd need to either reconstruct the networks manually without ViewScene, or edit the network XML file; neither are good solutions. The author/developer of BrainStimulator, Moritz (http://www.sci.utah.edu/people/moritz.html), should be able to get you further along in a way that makes sense for your needs. SCIRun 5-specific tutorials and help pages are also a bit lacking at this point, but we're still in "alpha" phase so that's to be expected. If you do come across any other issues on Ubuntu not related to ViewScene, you can file an issue here: https://github.com/SCIInstitute/SCIRun/issues/new
Dan

On 5/21/2015 10:09 AM, G Abouelseoud wrote:

Thank you very much for your reply.
Could you further clarify what do you mean by without visualization: Does this mean that GUI is not working or just the module "view"?
The crash occurs when I just try to open the tutorial network. If this means that I cannot use the GUI, could you further explain how I can use scirun 5 to process matrices and fields without the GUI (I have a good experience with programming, Thank God)?
Sorry to take much of your time and thank you for letting such a valuable software as Scirun available as open-source.

On 21 ماي, 2015 م 06:00, Daniel White wrote:

Unfortunately SCIRun 5's graphics renderer does not work on Linux right now. It's a known issue and is one of our top priorities, but has proven to be a difficult fix. The error messages below are just warnings and not related to the cause of the crash. You should still be able to use SCIRun 5 to process matrices and fields, but with no visualization we know it is not as useful for most people. Try using it on Windows or Mac for now, or just save output files to disk and visualize with SCIRun 4.7. And watch this page for future releases, for we will definitely announce there when we have it working on Linux: https://github.com/SCIInstitute/SCIRun/releases.

Thanks,
Dan

On Thu, 21 May 2015 10:55:35 +0200
G Abouelseoud <la.ilah.illa.allah@yandex.com> wrote:

Dear colleagues,
My best wishes ans sincere prayers to you all.
I am working with scirun 5 and brain stimulator on ubuntu trusty tahr. When ever I try to launch (load) the tdcs toy tutorial I get this error and scirun crashes:
QFont::setPointSizeF: Point size <= 0 (0.000000), must be greater than 0
QFont::setPointSizeF: Point size <= 0 (0.000000), must be greater than 0
QFont::setPointSizeF: Point size <= 0 (0.000000), must be greater than 0
QFont::setPointSizeF: Point size <= 0 (0.000000), must be greater than 0
Segmentation fault (core dumped)

I hope someone can help me.

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• [SCIRUN-USERS] regarding scirun 5 and brain stimulator, G Abouelseoud, 05/21/2015
  • Re: [SCIRUN-USERS] regarding scirun 5 and brain stimulator, Daniel White, 05/21/2015
    • Re: [SCIRUN-USERS] regarding scirun 5 and brain stimulator, G Abouelseoud, 05/21/2015
      • Re: [SCIRUN-USERS] regarding scirun 5 and brain stimulator, Dan White, 05/21/2015
        • Re: [SCIRUN-USERS] regarding scirun 5 and brain stimulator, G Abouelseoud, 05/30/2015

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