[Simnibs-discuss] Pathologies in head model

[Oula Puonti]

Hi Viktor,

We still do not have an automated segmentation method to handle tumors
or pathologies in the new version of simnibs, i.e., in charm.

However, adding pathologies to and existing head model is much easier
in the new version. You can either do it manually by editing the
segmentation directly or by using an automated segmentation from
another tool. Please see the steps here:

https://simnibs.github.io/simnibs/build/html/tutorial/advanced/fix_headmodel.html

and here:

https://simnibs.github.io/simnibs/build/html/documentation/command_line/add_tissues_to_upsampled.html#add-tissues-to-upsampled-doc

The first link shows how to manually edit the segmentation, whereas the
second one shows how to use a pre-existing segmentation from another
tool.

Best,
Oula



On Fri, 2023-02-03 at 01:16 +0100, Виктор Тимохов wrote:
> Dear SimNIBS Developers,
>  
> My name is Viktor Timokhov, and our team is developing ways to
> individualize stimulation protocols for patients based on SimNIBS. In
> the chapter "SimNIBS 2.1: A Comprehensive Pipeline for Individualized
> Electric Field Modelling for Transcranial Brain Stimulation" it was
> mentioned that
>  
> Neither mri2mesh nor headreco have off-the-shelf support for
> pathologies such as tumours or lesions. 
>  
> However, in SimNIBS 4.0 both methods were replaced with Charm. As I
> am still learning how do these methods work, I would like to ask a
> question: how did the situation on modeling brains with pathologies
> change with Charm?
>  
> Kind regards,
> Viktor Timokhov.
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss