EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software

Hosted by

Workshop: Introduction to EIDORS

Instructions

1. Compile and install a copy of netgen 5.0

   mkdir src
   cd src
   wget http://downloads.sf.net/project/netgen-mesher/netgen-mesher/5.0/netgen-5.0.0.zip
   unzip netgen-5.0.0.zip
   cd netgen-5.0.0
   # ENSURE we have apt-get install tk-dev tcl-dev libtogl-dev
   ./configure --prefix=$HOME/local
   make
   make install
   

2. Download and unzip the latest EIDORS release
   • eidors3.7RC.zip
3. Start Matlab, in a terminal

   export NETGENDIR=$HOME/local/bin
   export PATH=$HOME/local/bin:$PATH
   matlab
   

4. In matlab, do
   • run ~/Desktop/eidors-v3.7RC/eidors/startup.m
   • compare_2d_algs(1)
     (this tests if eidors is working)
   • show_fem(ng_mk_cyl_models(3,[0],[])) (this tests if netgen is working)
5. Get svn version of eidors

   cd 
   svn co svn://svn.code.sf.net/p/eidors3d/code/trunk eidors-svn
   

   In matlab run the new startup file

   run ~/eidors-svn/eidors/startup.m
   

Challenge problem:

1. Create a 3D elliptical cylinder with 16 circular electrodes (see here)
   fmdl= ng_mk_ellip_models([1,1.2,0.8],[16,0.5],[0.1]); show_fem(fmdl);
2. Put a ball into the elliptical cylinder
   extra={'ball','solid ball = sphere(0.5,0.5,0.5;0.1);'};
   fmdl= ng_mk_ellip_models([1,1.2,0.8],[16,0.5],[0.1],extra); show_fem(fmdl);
3. Put two balls into the elliptical cylinder
   extra={'ball','solid ball = sphere(0.5,0.5,0.5;0.1) or sphere(0.5,-0.5,0.5;0.1);'};
   fmdl= ng_mk_ellip_models([1,1.2,0.8],[16,0.5],[0.1],extra); show_fem(fmdl);
4. Set the model to use adjacent current patterns
   stim = mk_stim_patterns(16,1,[0,1],[0,1],{}); fmdl.stimulation = stim;
5. Simulate homogeneous voltages (background conductivity = 0.5);
   img = mk_image(fmdl, 0.5); vh = fwd_solve(img);
   show_fem(img);
6. Simulate inhomogeneous voltages (ball conductivity = 1.0);
   img.elem_data(fmdl.mat_idx{2})= 1.0; vi = fwd_solve(img);
   show_fem(img);
7. Reconstruct the image using GREITv1
   imdl= mk_common_gridmdl('GREITc1'); img= inv_solve(imdl,vh,vi);
   show_fem(img);
8. Create a GREIT model for the ellipse (see here)
   opt.noise_figure = 0.5; %other options are defaults
   imdl = mk_GREIT_model(mk_image(fmdl,0.5), 0.25, [], opt);
   img= inv_solve(imdl,vh,vi); show_fem(img);
9. Compare images for different stimulation patterns (see here)