Removing a lesioned area

[romboide2004]

For example by doing this: Removing a lesioned area - #15 by romboide2004

[Francois]

OK, got it. Thanks.

[romboide2004]

I was also wondering how exactly brainstorm behaves when setting up a DUNEuro head model. Specifically:

• "layer" and "surface" are not the same thing, right? I interpret "layer" as the volume of a certain segmented tissue.

• "Force source space inside layer "gray"": will the dipoles be forced to be either part of solely the gray matter tissue or within all the volume enclosed in the surface of such layer? The main difference between these two is that the first approach would let me exclude "empty spaces" in the cortex (e.g. lesion masks) from the source space and potentially avoid the known "source space is not convex" error.

Many thanks in advance.

[tmedani]

hey @romboide2004 it may be better to open a new discussion for this topic.

@romboide2004

ow exactly brainstorm behaves when setting up a DUNEuro head model.

it will use the FEM modeling to compute the forward solution.

@romboide2004

"layer" and "surface" are not the same thing, right? I interpret "layer" as the volume of a certain segmented tissue.

If you assume a volume mesh/model, then you are right. The layer can be the enclosed volume between two surfaces.

@romboide2004

"Force source space inside layer "gray"": will the dipoles be forced to be either part of solely the gray matter tissue or within all the volume enclosed in the surface of such layer?

if your model has a brain as one volume, all the dipole will be forced to be within this volume. If you distinguish the WM and GM, then BS will ask you to force diple within the GM.

[romboide2004]

@tmedani

it may be better to open a new discussion for this topic.

Sorry about that, I thought that these details might be relevant to correctly handle a lesion, which might potentially create empty spaces in the head model.

@tmedani

If you distinguish the WM and GM, then BS will ask you to force diple within the GM.

This is what is not totally clear to me. By "within" the GM, in a volume model, is it meant all the volume enclosed by the GM surface? If so, if a lesioned tissue is (partially) segmented within the volume enclosed by GM, that will also be included in the source space, right?

If this is the case, perhaps surface models might be more effective to address this issue and make sure dipoles are not in the lesion...

Thank you again,
Ramtin

[tmedani]

@romboide2004

This is what is not totally clear to me. By "within" the GM, in a volume model, is it meant all the volume enclosed by the GM surface? If so, if a lesioned tissue is (partially) segmented within the volume enclosed by GM, that will also be included in the source space, right?

Probably yes, if you have the final model, we can check it.
But for these specific cases, I recommend that you define a custom source space and then overlay it with the lesioned brain for visual checking.

[romboide2004]

I am not familiar with implementing a custom source space, which is why so far I relayed on Brainstorm for generating it. I might first try with a surface model (with which I should be able to only stick to the cortex and exclude anything else, I presume...), then explore how to build a custom source space.

Thank you for your help!