[Simnibs-discuss] Making models with burr holes

[Fang Cao]

Dear Steven,

On top of my last email, we recommend that you start with the option 2, so create the burr holes with mesh files directly. Option 1 is not available with the current version of SimNIBS. I am sorry for the confusion, but we are working on it now, and hopefully we will release the new version of SimNIBS next year so you could try option 1 too.

Best of luck,
Fang
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From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of Fang Cao <fang.cao at regionh.dk>
Sent: Tuesday, 19 October 2021 14.23
To: Beumer, Steven <s.beumer at tue.nl>; simnibs-discuss at drcmr.dk <simnibs-discuss at drcmr.dk>
Subject: Re: [Simnibs-discuss] Making models with burr holes

Dear Steven,

I do not know what you want to do with the simulation, but to simply answer your question, yes, we have done simulations of burr holes in vivo human brain with SimNIBS, but it needs some extra coding to create burr holes on the skull. For our purpose, we have done two different ways of simulation:

  1.  Start with the labeled image "m2m_<foldname>/label_prep/tissue_labeling_upsampled.nii.gz". We create the burrholes in the labeled image by relabeling the indices of the voxels that we want to label as burrholes, and then mesh it with Simnibs.
  2.  Start with the mesh file (*.msh). We create burr holes in the mesh file directly by changing the tags of the tetrahedra that we want to set as burr holes, then run the simulations.

Both ways can be done, and which way to go depends on what you want to do and how you want to do it. I hope it makes sense.

Best regards,
Fang
________________________________
From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of Beumer, Steven <s.beumer at tue.nl>
Sent: Monday, 18 October 2021 20.06
To: simnibs-discuss at drcmr.dk <simnibs-discuss at drcmr.dk>
Subject: [Simnibs-discuss] Making models with burr holes


Dear community,



First of all, thank you for answering all the questions that we have about SimNibs.

We were curious if anyone had tried to do simulations with burr holes in SimNibs, as been done in commercial software (Measurements and models of electric fields in the in vivo human brain during transcranial electric stimulation. Y. Huang et. Al.). If so, I would be interested in how the modeling was done and if there were any tips on it. Thanks in advance!



Sincerely,



Steven Beumer MSc

[TUe-logo-descriptor-line-scarlet-rgb]

PhD at the electrical engineering faculty







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________________________________


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