[FieldTrip] Forward solution using concentric spheres and BEM models

[Schönherr, Margit]

Hello,

I probably cannot help you with all your questions, but currently I'm also dealing with MRI segmentation and volume conductors, so maybe my solutions can be useful for you.
Concerning your point 5 (geometrical description of the brain, skull, and scalp), I have done it the following way:

cfg             = [];
cfg.method      = 'segmentation';
cfg.tissue      = [1 2 3]; % scalp = 1; skull = 2; brain = 3;
cfg.numvertices = [2000 1000 800];
cfg.sourceunits = 'mm';
cfg.mriunits    = 'mm';
bnd = ft_prepare_mesh(cfg, mri_segment);

I think you have to specify a vector 'cfg.numvertices', a number of vertices for each compartment.
By the way, at the beginning of ft_prepare_mesh the cfg-field 'numcompartments' is removed from the cfg structure (at least in my fieldtrip version, which is not the latest).

Another question that comes to me is, why you need the segmented MRI for a concentric spheres volume conductor? So, regarding point 6, you can build such a vol-structure for example like this:

vol.unit = 'm';
vol.o = origin;
vol.r = [R_brain R_skull R_skin];
vol.c = [1 1/80 1];

By this, you can also define the radius as you like.

Best,
Margit




________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von Juan Pablo Neira [jpnv2006 at gmail.com]
Gesendet: Mittwoch, 17. August 2011 14:58
An: fieldtrip at donders.ru.nl
Betreff: [FieldTrip] Forward solution using concentric spheres and BEM models

Hello,

I am working with an individual MRI and EEG data to do the forward
solution with two different volume's model (concentric spheres and
BEM),
so at the end i can compare the results.  But i did not have the
expected results of the concentric spheres model until now.

This is my script:

1.  Read individual MRI
mri=ft_read_mri('data_patient_1\******.hdr');

%I got this "Warning: flipping 1st dimension (L-R) to obtain volume in
neurological convention"

%How can i do a homogenous transformation matrix, using the voxel dimensions
%that are specified in hdr.dime.pixdim?

2. Realign to 'head coordinates'

3. MRI Reslicing

4. MRI segmentation: (brain, skull,scalp)

5. Create geometrical description of the brain, skull and scalp (3 compartments)

cfg                 = [];
cfg.interactive     = 'no';     %segmentation method
cfg.numvertices     = 3000;
cfg.sourceunits     = 'mm';
cfg.downsample      = 2;
cfg.numcompartments = 3;
cfg.tissue          = {'brain' 'skull' 'scalp'};
cfg.smooth          = 'yes';
bnd                 = ft_prepare_mesh(cfg, mri_segment);

%The output just give me the geometrical description of the brain.
How can i get the geometrical description of
%the skull and scalp also to proceed to create a 3 spheres concentric
sphere model?

6.  If i have the 3 geometrical descriptions (brain, skull and scalp).
 Create a 3 concentric spheres model.

cfg                 = [];
cfg.headshape       = [bnd1 bnd2 bnd3];   % brain- skull - scalp
cfg.conductivity    = [0.33 0.0042 0.331];
[vol, cfg]          = prepare_concentricspheres(cfg);

%I got the model but part of the brain is outside of its sphere and
also the skull.  How can I increase the radius so
% the whole brain will be inside its sphere and also the skull?  The
sphere of the scalp fix good.

I hope someone can help me solve these questions.

Regards,

Juan Pablo

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