EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software

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GREIT Reconstruction with IBEX software

This tutorial describes how to reconstruct data and create an IBEX compatible file.

Create Reconstruction Matrix and ROIs

fmdl= mk_library_model('adult_male_16el_lungs');
img = mk_image(fmdl, 1); % background conductivity
img.elem_data(fmdl.mat_idx{2}) = 0.3001; % lungs
img.elem_data(fmdl.mat_idx{3}) = 0.3002; % lungs
ROI = calc_slices(img,[inf,inf,0.5]);
llung_ROI = ~isnan(ROI) & (ROI==0.3001);
rlung_ROI = ~isnan(ROI) & (ROI==0.3002);
thorax_ROI= ~isnan(ROI); % include lungs, too

subplot(131); imagesc(thorax_ROI); axis image
subplot(132); imagesc(rlung_ROI);  axis image
subplot(133); imagesc(llung_ROI);  axis image
print_convert('GREIT_IBEX_01a.png');

Figure:

[stim,msel] = mk_stim_patterns(16,1,[0,1],[0,1],{'no_meas_current'},1);
img.fwd_model.stimulation = stim;
img.fwd_model = mdl_normalize(img.fwd_model, 1);
opt.imgsz = [64 64];
opt.distr = 3;
opt.Nsim = 500;
opt.target_size = 0.03;
opt.target_offset = 0;
opt.noise_figure = .5; 
opt.square_pixels = 1;
imdl=mk_GREIT_model(img, 0.25, [], opt);
imdl.fwd_model.meas_select = msel;

Load and reconstruct Data

fname = 'DATA/STUDYNAME/SUBJECT_1/YYYYMMDD/Eit/Viasys/1001_c4.get';
vv= eidors_readdata(fname);
img= inv_solve(imdl, mean(vv,2), vv);

imgs= -calc_slices(img); % Negative to air is +
imgs(isnan(imgs(:)))= 0;

img.calc_colours.ref_level=0;
img.elem_data = img.elem_data(:,2:4:120);
img.show_slices.img_cols = 10;
clf; show_slices(img);

print_convert 'GREIT_IBEX_03a.jpg'

Figure: Example Images of reconstructed data

Create the required variables to use IBEX

data.imageRate = 13;

data.patient.ROI.Inside =thorax_ROI*100; % to scale it up to 100
data.patient.ROI.RightLung =rlung_ROI*100;
data.patient.ROI.LeftLung =llung_ROI*100;
data.patient.ROI.Heart =zeros(size(imgs,1),size(imgs,2));

% put to dummy because they are missing
data.patient.halfChest = 'NaN';
data.patient.height = 'NaN';
data.patient.weight = 'NaN';
data.patient.gender = 'NaN';

data.measurement.Position.transversal = zeros (1,size(imgs,3));
data.measurement.Position.longitudinal = zeros (1,size(imgs,3));
data.measurement.ImageQuality = 100*ones(1,size(imgs,3));
data.measurement.ElectrodeQuality = zeros(size(imgs,3),32);
data.measurement.ZeroRef = imgs;

data.injctionPattern= 'NaN';
data.SensorBelt.NumEl= 'NaN';

data.measurement.CompositValue=squeeze(sum(sum(imgs,2),1));

save('file-for-IBEX.mat','data');

Figure: IBEX software using these data