Meshing the electrode sheet within brain mesh model

Hi,
I am using brainstorm to get the mesh. My question is, Is there any way to add the electrode sheet inside the mesh, making it part of the tetrahedral mesh or hexahedral mesh.

as you can see in the following figure that one unwarped braintorm the as the electrode sheet was not part of the mesh with 0 conductivity the potential isnt 0 at that point.

Can I have the electrode sheet model purple within the meshed brain.
image

regards,
Saima Safdar

Hi Saima,

You have here a particular example with a complete electrode model. The current version of Brainstorm cant handle this specific case.

A possible solution is to use the volume masks (segmentation) of you model (including the head tissues and the electrode body), then you can construct the tetrahedral/hexa mesh from the masks. You can check the iso2mesh toolbox and particularity the function "vol2mesh" .

Let us know the results, Brainstom may add this feature in the future.

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Hi,
What is the extension for volume mask (segmentation) to be imported into brainstorm?

We are working in 3D Slicer. May I know what file extensions are required for volume masks (segmentation) so it can be imported into brainstorm?

Regards,
Saima Safdar

Brainstorm can read multiple volume format:
MRI volumes

  • Analyze (.img/.hdr)
  • BrainVISA GIS (.ima/.dim)
  • CTF (.mri)
  • DICOM (using SPM converter)
  • MINC (.mnc)
  • MGH (.mgh, .mgz)
  • Neuromag (.fif)
  • Nifti-1 (.nii, .nii.gz)

You can also put your data in the matlab format that Brainstorm support for the "tissue",
you need to have an example in your database, then export it to matlab to see the format.

as in this picture:
image

image

Hi,
could you please provide any steps to do for using isotomesh.

I have a segmentation map with electrode sheet inside as nifti image.
Do i need to load masks seperately and what file extension.

I have uploaded all the masks as nii.gz but when i select all the mris I do not see option for meshing. the loaded files looks like as in figure.

image

Regards,
Saima Safdar

Hi,

As I mentioned before, this is a specific case which is not supported by the available functions in Brainstorm yet. You need to use a custom script for your specific case.

What I can recommend is to merge all the masks together and then use the iso2mesh functions to generate the tetrahedral mesh.

Please refer to the function vol2mesh

Check also the "samples" folder here:

where basic scripts are used:
image

You need to adapt these script for you specific application.

1 Like

Hey @saimasafdar,

Were you able to generate the complete electrode mesh with he iso2mesh functions?

Thanks,

Hi,
No not yet. We have generated mesh using our framework and got the forward problem results and we used our volume conductor model to get forward problem results using duneuro. we compared these two results. I will share the results once finalized.

Regards,
Saima Safdar