Use user defined cortical mesh?

[Rachel S]

Hi all, 

I try to use my own cortex surface generated in Brainstorm. I get the Vertices.txt, Vertex_normals,txt and triangles.txt and use 

mycortex = cortex.Cortex.from_file(source_file='cortex_5001.zip') to load the cortex. But when I configure it, it broke down at gdist.local_gdist_matrix function.

Here is my .zip and the Brainstorm cortex I use. Is this the right way to define our own cortex? Is there anything that I missed? Thank you in advance.

Best,

Rachel

[WOODMAN Michael]

Hi

 

The ZIP looks OK, what was the error?

 

Thanks,

Marmaduke

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[Rachel S]

Hi Marmaduke,

If I used compiled version on Windows, and ran the code with Ipython_notebook.bat, it said "the kernal appears to have died.". Then I installed from Github on another Win machine, and ran the code in Pycharm, it said "process finished with exit code -1073740777 (0xC0000417)". It happened at gdist.local_gdist_matrix. Do you know if this is a common issue for Windows machines? Since I tried two Win machines. Thank you.

Best,

Rachel

WOODMAN Michael <marmaduk...@univ-amu.fr> 于2019年3月18日周一 上午4:37写道：

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[WOODMAN Michael]

Hi

 

Thanks, that’s a generic error, that may be due to the gdist extension not working correctly.  I would guess that it runs out of memory.  If I remember correctly, a 16k vertex surface requires 1-2 GB of memory . Do you have enough memory?  You can watch in the Task Manager, under the Performance tab, the memory, while running this, and see if your computer is running out of memory.

 

Cheers,

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[Rachel S]

Hi,

Thank you for your quick response and suggestions. I can generate the local connectivity matrix for 16k cortex. Everything runs smoothly when I use the default files. The problem happens when I try to use my own, coarser cortex.

Best,

Rachel

WOODMAN Michael <marmaduk...@univ-amu.fr> 于2019年3月18日周一 上午11:13写道：

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[WOODMAN Michael]

Hi

 

Perhaps, or TVB is making using of the pregenerated cortex.  How many vertices are in your cortex?

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[Rachel S]

Hi,

My cortex has 5001 vertices. 

And I also tried using linux, it broke out with "segmentation fault (core dumped)". I tried many cortex generated with different softwares, and your mesh is the only one that works. May I ask how do you generate your cortex mesh for the tutorial? Is there any requirement on the mesh that I do not know of? Have you guys tried to use a smaller mesh before? Thank you so much. 

Best,

Rachel

WOODMAN Michael <marmaduk...@univ-amu.fr> 于2019年3月19日周二 上午4:59写道：

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[WOODMAN Michael]

Hi

 

That’s odd, sorry to hear it’s not working.  Is there any chance you can send me privately just the cortex zip file so I can test it? (marmaduk...@univ-amu.fr)

 

Usually we generate meshes from FreeSurfer pial surfaces, resamping to fsaverage5 resolution (10k per hemisphere), so 5k vertices should work fine, but if there are any holes in the surface, for example, maybe that causes a problem.

 

Cheers,

marmaduke

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