Merge pull request fieldtrip#743 from sarangnemo/master

move testOpenMEEGeeg.m to test folder

test/test_openmeeg_eeg.m

@@ -0,0 +1,134 @@
+function test_openmeeg_eeg
+
+% TEST test_openmeeg_eeg
+% (previously called testOpenMEEGeeg)
+% Test the computation of an EEG leadfield with OpenMEEG
+
+% Copyright (C) 2010-2017, OpenMEEG developers
+
+addpath(pwd) % Make sure current folder is in the path
+
+%% Set the position of the probe dipole
+dippos = [0 0 70];
+
+%% Set the radius and conductivities of each of the compartments
+
+% 4 Layers, defined from outside to inside (i.e., [scalp skull CSF brain])
+r = [100 92 88 85];
+c = [1 1/80 1/20 1];
+
+[rdms,mags] = run_bem_computation(r,c,dippos);
+
+% the following would require the installation of xunit toolbox
+% assertElementsAlmostEqual(rdms, [0.019963 0.019962 0.10754], 'absolute', 1e-3)
+% assertElementsAlmostEqual(mags, [0.84467 0.84469 0.83887], 'absolute', 1e-3)
+
+%use instead
+thr = 2e-2;
+assert(norm(rdms-[0.019963 0.019962 0.10754])<thr)
+assert(norm(mags-[0.84467 0.84469 0.83887])<thr)
+
+% 3 Layers, defined from outside to inside (i.e., [scalp skull brain])
+r = [100 92 88];
+c = [1 1/80 1];
+
+[rdms,mags] = run_bem_computation(r,c,dippos);
+% assertElementsAlmostEqual(rdms, [0.064093 0.064092 0.13532], 'absolute', 1e-3)
+% assertElementsAlmostEqual(mags, [1.0498 1.0498 1.0207], 'absolute', 1e-3)
+assert(norm(rdms-[0.064093 0.064092 0.13532])<thr)
+assert(norm(mags-[1.0498 1.0498 1.0207])<thr)
+
+% 2 Layers, defined from outside to inside
+r = [100 92];
+c = [1/4 1];
+
+[rdms,mags] = run_bem_computation(r,c,dippos);
+% assertElementsAlmostEqual(rdms, [0.15514 0.15514 0.1212], 'absolute', 1e-3)
+% assertElementsAlmostEqual(mags, [1.8211 1.8211 1.3606], 'absolute', 1e-3)
+assert(norm(rdms-[0.15514 0.15514 0.1212])<thr)
+assert(norm(mags-[1.8211 1.8211 1.3606])<thr)
+
+% 1 Layer
+r = [100];
+c = [1];
+
+[rdms,mags] = run_bem_computation(r,c,dippos);
+% assertElementsAlmostEqual(rdms, [0.18934 0.18931 0.0778], 'absolute', 1e-3)
+% assertElementsAlmostEqual(mags, [1.3584 1.3583 1.2138], 'absolute', 1e-3)
+assert(norm(rdms-[0.18934 0.18931 0.0778])<thr)
+assert(norm(mags-[1.3584 1.3583 1.2138])<thr)
+
+
+function [rdms,mags] = run_bem_computation(r,c,dippos)
+
+    %% Description of the spherical mesh
+    [pos, tri] = icosahedron42;
+    % [pos, tri] = icosahedron162;
+    % [pos, tri] = icosahedron642;
+
+    %% Create a set of electrodes on the outer surface
+    sens.elecpos = max(r) * pos;
+    sens.label = {};
+    sens.unit = 'mm';
+    nsens = size(sens.elecpos,1);
+    for ii=1:nsens
+        sens.label{ii} = sprintf('vertex%03d', ii);
+    end
+
+    %% Create a triangulated mesh, the first boundary is outside
+    bnd = [];
+    for ii=1:length(r)
+        bnd(ii).pos = pos * r(ii);
+        bnd(ii).tri = tri;
+    end
+
+
+    %% Compute the BEM model
+    cfg = [];
+    cfg.method = 'openmeeg';
+
+    % vol structure only needs these elements;
+    % ft_prepare_headmodel should *not* be used!
+    vol_bem = [];
+    vol_bem.bnd = bnd;
+    vol_bem.cond = c;
+    vol_bem.type = 'openmeeg';
+
+    % ft_prepare_headmodel has a bug; likely the geom file does not match
+    % the true order of the layers
+    %cfg.conductivity = c;
+    %vol_bem = ft_prepare_headmodel(cfg, bnd);
+    %
+    % though, removing the computed headmodel matrix makes it work, as a hack:
+    %vol_bem = rmfield(vol_bem,'mat');
+
+    cfg.vol = vol_bem;
+    cfg.grid.pos = dippos;
+    cfg.grid.unit = 'mm';
+    cfg.elec = sens;
+    grid = ft_prepare_leadfield(cfg);
+
+    lf_openmeeg = grid.leadfield{1};
+
+    % Rq : ft_compute_leadfield centers the forward fields by default
+    % (average reference)
+    % lf_openmeeg = lf_openmeeg - repmat(mean(lf_openmeeg),size(lf_openmeeg,1),1);
+
+    %% Compute the analytic leadfield
+    vol_sphere = [];
+    vol_sphere.r = r;
+    vol_sphere.cond = c;
+    lf_sphere = ft_compute_leadfield(dippos, sens, vol_sphere);
+
+    %% Evaluate the quality of the result using RDM and MAG
+    rdms = zeros(1,size(lf_openmeeg,2));
+    for ii=1:size(lf_openmeeg,2)
+        rdms(ii) = norm(lf_openmeeg(:,ii)/norm(lf_openmeeg(:,ii)) - lf_sphere(:,ii) / norm(lf_sphere(:,ii)));
+    end
+    mags = sqrt(sum(lf_openmeeg.^2))./sqrt(sum(lf_sphere.^2));
+    disp(['RDMs: ',num2str(rdms)]);
+    disp(['MAGs: ',num2str(mags)]);
+
+end %  function
+
+end