[FieldTrip] Forward solution using concentric spheres and BEM models

[Juan Pablo Neira]

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