[Simnibs-discuss] Making models with burr holes

Fang Cao fang.cao at regionh.dk
Tue Oct 19 14:23:20 CEST 2021

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,
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!


Steven Beumer MSc


PhD at the electrical engineering faculty


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