Mislabeling of tissues using SimNIBS charm

Discussions
1

Hello BrainStorm Team,

I hope you are all well!

I have been running the SimNIBS charm function on T1 MRIs of participant's with surgical cavities. The labeling of the different tissues has worked well for some but not all.

Sometimes, the surgical cavities are marked as grey matter rather than CSF (see example image below).

Can this be rectified manually or with altering some settings when launching charm? Would adding a T2 MRI help with the segmentation?

Any guidance would deeply be appreciated!

mislabeled_CSF_as_GM
mislabeled_CSF_as_GM290×314 44 KB

Best wishes,
Ellie

2

@tmedani, do you have any advise on this topic?

1 Like
3

Hi @EHill

The automatic mesh generation assumes a healthy and normal brain.

This is documented in the main Brainstorm FEM paper:

image
image1219×226 29.4 KB

For such cases, you need to do manual checking on the surfaces before the generation of the FEM mesh. You can edit and manipulate the intermediates surfaces using some tools like MeshLab, VTK or similar tools.

You can also check with the SimNibs team if they can provide better recommendations: Issues · simnibs/simnibs · GitHub

Best,
Takfarinas