Eidors-logo    

EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software

EIDORS (mirror)
Main
Documentation
Tutorials
− Image Reconst
− Data Structures
− Applications
− FEM Modelling
− GREIT
− Old tutorials
Workshop
Download
Contrib Data
GREIT
Browse Docs
Browse SVN

News
Mailing list
(archive)
FAQ
Developer
                       

 

Hosted by
SourceForge.net Logo

 

GREIT Reconstruction for an neonate human thorax geometry

Data

Data are available Here. Data were recorded from a 10-day old spontaneously breathing neonate lying in the prone position with the head turned to the left, as documented in: S. Heinrich, H. Schiffmann, A. Frerichs, A. Klockgether-Radke, I. Frerichs, Body and head position effects on regional lung ventilation in infants: an electrical impedance tomography study. Intensive Care Med., 32:1392-1398, 2006.

Subject Image:

Image reconstruction model

Forward model model
% Inverse model
%fmdl = mk_library_model('neonate_16el_lungs');
elec_pos = [16,1,.5]; elec_shape=[0.15,0.3,0.01,0,60]; maxsz=0.08; nfft=27;
fmdl = mk_library_model({'neonate','boundary','left_lung','right_lung'}, ...
      elec_pos, elec_shape, maxsz,nfft);

[fmdl.stimulation fmdl.meas_select] = mk_stim_patterns(16,1,'{ad}','{ad}');
fmdl = mdl_normalize(fmdl,1);

img = mk_image(fmdl,1); img.elem_data(vertcat(fmdl.mat_idx{2:3})) = 0.3;
img.calc_colours.ref_level=1;

calc_colours('defaults');
show_fem_enhanced(img); view(-2,32)
print_convert neonate_ex01a.jpg


Figure: Finite element model of thorax
Reconstruction model
img = mk_image(fmdl,1); img.elem_data(vertcat(fmdl.mat_idx{2:3})) = 0.6;
opt.square_pixels = 1; opt.imgsz = [64 64];
%opt.noise_figure = 0.5;
%imdl = mk_GREIT_model(img, 0.20, [], opt);
imdl = mk_GREIT_model(img, 0.20, 10, opt);

GREIT reconstruction

Reconstruct images
% Data: eidors3d.sf.net/data_contrib/if-neonate-spontaneous/if-neonate-spontaneous.zip
vv= eidors_readdata('P04P-1016.get');

% solve with reference to the mean
imgall = inv_solve(imdl,mean(vv,2),vv);
[insp, expi] = find_frc(imgall,[],13,[],2); % find breaths

% use expirations as reference
imgr = inv_solve(imdl,vv(:,expi),vv(:,insp(2:end)));
   imgr.calc_colours.ref_level= 0;
   imgr.calc_colours.backgnd= [1 1 1];
   imgr.calc_colours.greylev= 0.001;
   imgr.show_slices.img_cols = 4;
   imgr.show_slices.sep      = 2;
show_slices(imgr);

print_convert neonate_ex03a.png


Figure: Images of three different breaths (end inspiration)
Reconstruct temporal signals
%%BUG. NEED TO FIND IMGALL.

% positions of where to plot
yposns = [20 20 45 45];
xposns = [20 45 20 45];

% Show image
clf; axes('position',[0.05,0.5,0.25,0.45]);
img1= imgall; img1.elem_data = imgall.elem_data(:,45);
show_slices(img1);
hold all;
for i = 1:4
    plot(xposns(i),yposns(i),'s','LineWidth',5);
end
hold off;

% Show plots
imgs = calc_slices(imgall);
axes('position',[0.32,0.6,0.63,0.28]);

imgs = permute(imgs,[3,1,2]);
taxis =  (0:size(imgs,1)-1)/13; % frame rate = 13
hold all
for i = 1:4
    plot(taxis,imgs(:,yposns(i),xposns(i)),'LineWidth',2);
end
hold off
set(gca,'ytick',[]);
xlim([0 16]);

print_convert neonate_ex03a.png


Figure: (bottom) time course of several lung pixels

Use Elliptic GREIT model

The shape of a neonate is roughly elliptical. Based on the neonate CT here, the elliptical ration is about 1:1.14.
clf
n_elecs = 16;

% Elliptic model
[fmdle,midx] = ng_mk_ellip_models([1, 1.14,1,0.15] ,[n_elecs,0.5],[0.05]);
[stim,msel] =  mk_stim_patterns(n_elecs,1,[0,1],[0,1],{'no_meas_current'}, 1);
fmdle.stimulation =  stim;       
fmdle.meas_select =  msel;       
fmdle = mdl_normalize(fmdle, 1);

% GREIT Ellip - circ objects
opt.distr = 0; % central
opt.noise_figure = 0.5;
imdl = mk_GREIT_model(mk_image(fmdle,1), 0.25, [], opt);

vh = mean(vv,2);        % reference is average
vi = vv(:,[45,70,173]); %3 inspirations

img = inv_solve(imdl,vh,vi);

img.show_slices.img_cols = 3;
img.show_slices.sep      = 2;
img.calc_colours.ref_level=0;
show_slices(img);

print_convert neonate_ex04a.png


Figure: Images of lungs using ellipcal GREIT reconstruction

Last Modified: $Date: 2017-02-28 13:12:08 -0500 (Tue, 28 Feb 2017) $ by $Author: aadler $