EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software

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Internal electrodes

Electrode in a hole in the model

shape_str = [ ...
  'solid hole = sphere(0.2,0.2,1.5;0.08);' ... 
  'solid cyl    = cylinder (0,0,0; 0,0,1; 1) and not hole; \n', ...
  'solid mainobj= orthobrick(-2,-2,0;2,2,2) and cyl -maxh=0.3;\n'];
th = linspace(0,2*pi,7)'; th(end) = []; cs = [cos(th), sin(th)];
elec_pos = [  cs, th/2/pi + 0.5, cs, 0*th];
elec_shape=[0.1]; elec_obj = 'cyl';
fmdl = ng_mk_gen_models(shape_str, elec_pos, elec_shape, elec_obj);

% Put an electrode in the hole
el_nodes = fmdl.nodes - ones(num_nodes(fmdl),1)*[0.2,0.2,1.5];
shim = 1e-4; % a little bit extra to catch elements
el_nodes = sum(el_nodes.^2,2) <= .08^2 + shim;
fmdl.electrode(end+1) = struct( ...
    'nodes', find(el_nodes), ...
    'z_contact',.01);

show_fem(fmdl); view(90,60);
print_convert internal_electrodes01a.jpg

Figure: Internal electrode using a hole in the model.

Specifying the electrode boundary to EIDORS

extra={'ctr_el','solid ctr_el = sphere(0.2,0.2,0.5;0.08);'};
fmdl = ng_mk_cyl_models(1,[8,0.5],0.1,extra);


% Get electrode boundary
ctr_elec = fmdl.elems(fmdl.mat_idx{2},:);
bdy_elec = find_boundary(ctr_elec);
elec_nod = unique(bdy_elec(:));
fmdl.electrode(end+1) = struct( ...
     'nodes', elec_nod, 'z_contact',.01);
% Make sure EIDORS knows you have internal electrodes
fmdl.system_mat_fields.CEM_boundary = bdy_elec;

show_fem(fmdl); view(90,60);
print_convert internal_electrodes02a.jpg

Figure: Internal electrode by specifying using CEM_boundary

fmdl.stimulation = stim_meas_list([1,num_elecs(fmdl),1,2]);

img= mk_image(fmdl,1);
img.fwd_solve.get_all_meas = true;
vh=fwd_solve(img);

imgh = rmfield(img,'elem_data');
imgh.node_data = vh.volt;
show_slices(imgh,1); %center slice

print_convert internal_electrodes03a.jpg

Figure: Voltages in a slide of a model with internal electrode