[FieldTrip] Including brain lesion - OpenMeeg

[Sarang S. Dalal]

Dear Stefano,

OpenMEEG can do what you need. We wrote the function in FieldTrip that sets up the OpenMEEG parameters (fieldtrip/forward/private/leadfield_openmeeg.m) with the assumption that there would be either 3 layers (scalp, skull, brain) or 4 layers (scalp, skull, csf, brain). These layers are assumed to be nested from outside to inside, with no surfaces crossing or touching.

As Simon suggested, you probably have lesion nested within brain. So, if you don't have a CSF layer, you could use the 4-layer functionality that is already there, with the order [scalp skull brain lesion]. You will have to configure cfg.conductivity appropriately with the same order.

You may also take a look at the examples from my group where we script MRI segmentations and set up OpenMEEG computations in practice (for 3- and 4-layer nested geometries):
https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_mriproc.m
https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_makeleadfield.m

OpenMEEG will also support non-nested configurations, but you will have to adapt leadfield_openmeeg.m to get it to work with FieldTrip. You can have a look at the documentation on the OpenMEEG website for a description of how to write the parameter files for that situation.

Cheers,
Sarang

On Fri, 2017-12-15 at 11:12 +0100, Simon Homolle wrote:
Dear Stefano,

What do you mean by strange results? Some figures describing the results would help to give you further help.
You talked about 4 layers so i presume you used Skin, Skull, Brain and Lesion? Are these nested compartments? Could you show some visualisation of the meshes/segmentations you used?


seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed');

cfg              = [];
cfg.funparameter = 'seg';
cfg.funcolormap  = lines(6); % distinct color per tissue
cfg.location     = 'center';
cfg.atlas        = seg_i;    % the segmentation can also be used as atlas
ft_sourceplot(cfg, seg_i);


Best regards,

Simon Homölle
PhD Candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Phone: +31-(0)24-36-65059

On 15 Dec 2017, at 10:51, Stefano Caschera <caschera at dis.uniroma1.it<mailto:caschera at dis.uniroma1.it>> wrote:
Hi,
I would like to include a brain lesion to obtain a leadfield through openmeeg.

I have already computed the meshes.

Is it possible to use ft_prepare_headmodel and openmeeg_dsm ?
And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one.

If it is not possible using openmeeg, can you suggest me another method?

Thank you,
Stefano

--
Stefano Caschera, PhD Student

Neuroelectrical Imaging and BCI lab
Fondazione Santa Lucia, IRCCS
Via Ardeatina, 306
I-00179, Rome, Italy

Department of Computer, Control, and
Management Engineering "Antonio Ruberti"
Sapienza, University of Rome
V. Ariosto, 25
00185, Rome, Italy

Tel +39 06 5150 1165<tel:%2B39%2006%205150%201165>
Email: stefano.caschera at uniroma1.it<mailto:jlenia.toppi at uniroma1.it>
          caschera at dis.uniroma1.it<mailto:anzolin at dis.uniroma1.it>
          s.caschera at hsantalucia.it<mailto:j.toppi at hsantalucia.it>
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