EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software

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PEEP trial after lung injury (pig)

Methods and Data

Data were published in Frerichs, I., Dargavillle, P.A., Dudykevych, T., Rimensberger, P.M. (2003) Electrical Impedance Tomography − a method for monitoring regional lung aeration and tidal volume distribution? Intensive Care Med. 29:2312-2316, 2003.

Results

EIDORS Analysis

1. Download the data and save it to your working directory.
2. Create a FEM model of the pig

   % Create Model $Id: if_peep_trial01.m 3371 2012-07-02 09:08:43Z bgrychtol $
   
   fmdl = mk_library_model('pig_23kg_16el');
   [fmdl.stimulation fmdl.meas_select] = mk_stim_patterns(16,1,'{ad}','{ad}');
   fmdl = mdl_normalize(fmdl, 1);  % Use normalized difference imaging
   opt.noise_figure = 0.5; opt.imgsz = [64 64];
   imdl = mk_GREIT_model(fmdl, 0.25, [], opt);
   
   % subplot(211);
   show_fem(imdl.fwd_model, [0,1,0]);
   axis equal; axis off
   
   hh=text(-1.1,0,'Right');
   set(hh,'Rotation',90,'HorizontalAlignment','Center');
   hh=text(0,-1.15,'Ventral');
   set(hh,'HorizontalAlignment','Center');
   
   print_convert if_peep_trial01.png
   
   

   
   Figure: 3D FEM of pig thorax
3. Reconstruct images

   % Reconstruct Images $Id: if_peep_trial02.m 1535 2008-07-26 15:36:27Z aadler $
   
   v_injury = eidors_readdata('p1130107.get');
   r_injury = mean(v_injury(:,1:10),2); % reference meas
   v_treat  = eidors_readdata('p1130122.get');
   r_treat  = mean(v_treat(:,1:10),2); % reference meas
   
   i_injury = inv_solve(imdl, r_injury, v_injury);
   i_treat  = inv_solve(imdl, r_treat , v_treat );
   
   

4. Select Regions of interest to plot

   % Select ROI's
   
   img = i_injury; img.elem_data = img.elem_data(:,700);
   rimg = calc_colours( calc_slices( img ), img);
   
   np= calc_colours('npoints');
   xlocn= 5/16 * np;
   ylocn= [4:2:10]/16 * np; 
   for yl = 1:4;
      rimg(ylocn(yl) + (-2:2), xlocn + (-2:2) ) = 1;
   end
   image(rimg); axis square
   
   for yl = 1:4;
      text(xlocn-1, ylocn(yl), num2str(yl));
   end
   
   axis off
   print_convert if_peep_trial03.png
   
   

   
   Figure: Image of ventilation and 4 identified points to analyse regional ventilation
5. Normalized Impedance Change (ΔZ) at each ROI

   % Display Times courses $Id: if_peep_trial04.m 5788 2018-05-21 22:35:48Z aadler $
   
   for loop = 1:2;
      if loop == 1; img = i_injury;
      else          img = i_treat;
      end
   
      subplot(2,2,loop);
      time = (0:size(img.elem_data,2)-1)/13; % Frame rate = 13/s
   
      raster= calc_slices( img );
      ROIs  = raster(ylocn, xlocn, :);
      ROIs  = permute(ROIs, [3,1,2]);
   
      %Normalize to its maximum
      for i=1:length(ylocn)
         ROIs(:,i) = - ROIs(:,i) / max(abs(ROIs(:,i)));
      end
      plot(time, ROIs);
      axis([0, max(time), -0.1, 1]);
      legend('1','2','3','4','Location','NorthWest')
      xlabel('time (s)')
      ylabel('normalized \Delta Z')
   end
   
   print_convert if_peep_trial04.png '-density 175'
   
   

   
   Figure: Normalized ΔZ time course for different lung ROIs. Left Lung Injury Right Treated
6. Animate Output for each condition This function creates a video of the sample sequences.

   % Show images $Id: if_peep_trial05.m 1535 2008-07-26 15:36:27Z aadler $
   
   for loop = 1:2;
      if loop == 1; img = i_injury; fn= 'a';
      else          img = i_treat;  fn= 'b';
      end
   
      % image properties
      img.calc_colours.npoints     = 32;
      img.calc_colours.window_range= .5;
      img.calc_colours.ref_level   = 0;
      img.calc_colours.greylev     = 0.01;
      img.calc_colours.backgnd     = [1,1,1];
      img.animate_reconstructions.show_times = 1;
   
      animate_reconstructions(['if_peep_trial05',fn], img);
   end
   
   

   
   Figure: Video of sample sequences Left Lung Injury Right Treated