Hello,<br><br>I am a new user of fieldtrip. I am trying to generate BEM
system matrix using the function 'prepare_bemmodel' and the 'bemcp'
method. The system matrix 'vol.mat' I obtained using the following code
is a 'NaN' matrix.<br>
<br>%% -------------- Begin --------------<br>% ---- load brain mesh<br>% load_bnd is a function to load brainvisa mesh<br>[vol.bnd(1).pnt vol.bnd(1).tri] = load_bnd('../data/mesh/colin_<div>no_artef.eeg-3.bnd');<br>
vol.bnd(1).tri = vol.bnd(1).tri + 1;<br>
vol.bnd(1).pnt = vol.bnd(1).pnt;<br><br>% ---- load skull mesh<br>[vol.bnd(2).pnt vol.bnd(2).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-2.bnd');<br>vol.bnd(2).tri = vol.bnd(2).tri + 1;<br>vol.bnd(2).pnt = vol.bnd(2).pnt/1000;<br>
<br>% ---- load skin mesh<br>[vol.bnd(3).pnt vol.bnd(3).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-1.bnd');<br>vol.bnd(3).tri = vol.bnd(3).tri + 1;<br>vol.bnd(3).pnt = vol.bnd(3).pnt;<br><br>% ---- check meshes<br>
figure; triplot(vol.bnd(1).pnt, vol.bnd(1).tri, [], 'faces_skin'); rotate3d<br>figure; triplot(vol.bnd(2).pnt, vol.bnd(2).tri, [], 'faces_skin'); rotate3d<br>figure; triplot(vol.bnd(3).pnt, vol.bnd(3).tri, [], 'faces_skin'); rotate3d<br>
% this gives good results, so meshes are correctly loaded<br><br>% ---- prepare BEM model<br>vol.cond = [0.3300 0.0825 0.3300]; % conductivities<br>vol.skin = 3; % index of skin surface<br>cfg = [];<br>cfg.method = 'bemcp';<br>
vol = prepare_bemmodel(cfg, vol);<br>%% ------------------- End ------------------------<br><br>When executing this code I've got the following result in the matlab prompt<br><br>using the mesh specified in the input volume conductor<br>
determining source compartment (1)<br>determining skin compartment (3)<br>not using the isolated source approach<br>Nvert = 1222<br>Ntri = 2440<br>weight = 0.095493 , defl = 0.000000 <br>Nverta = 1222<br>Ntrib = 2440<br>
<br>Nverta = 1222<br>Ntrib = 2440<br>Nvert = 1222<br>Ntri = 2440<br>weight = -0.095493 , defl = 0.000000 <br>Nverta = 1222<br>Ntrib = 2440<br>Warning: Matrix is singular, close to singular or badly scaled.<br> Results may be inaccurate. RCOND = NaN. <br>
> In prepare_bemmodel at 187<br> In test_fieldtrip at 166<br>Nverta = 1222<br>Ntrib = 2440<br>Warning: Matrix is singular, close to singular or badly scaled.<br> Results may be inaccurate. RCOND = NaN. <br>> In prepare_bemmodel at 194<br>
In test_fieldtrip at 166<br>Nverta = 1222<br>Ntrib = 2440<br>Nverta = 1222<br>Ntrib = 2440<br>Nvert = 1222<br>Ntri = 2440<br>weight = 0.159155 , defl = 0.000818 <br>Warning: Matrix is singular, close to singular or badly scaled.<br>
Results may be inaccurate. RCOND = NaN. <br>> In prepare_bemmodel at 220<br> In test_fieldtrip at 166<br><br>and
as I mentionned the resulting BEM system matrix vol.mat is a 'NaN'
matrix. I guess the problem occurs in this part of the prepare_bemmodel
function (beginning at line 152):<br>
<br> % --------------------------------------------<br> % Deal first with surface 1 and 2 (inner and outer skull<br> <br> % NOTE:<br> % C11st/C22st/C33st are simply the matrix C11/C22/C33 minus the identity<br> % matrix, i.e. C11st = C11-eye(N)<br>
<br> weight = (vol.cond(1)-vol.cond(2))/((vol.cond(1)+vol.cond(2))*2*pi);<br> C11st = bem_Cii_lin(vol.bnd(1).tri,vol.bnd(1).pnt, weight,defl(1),vol.bnd(1).pnt4);<br> weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3))*2*pi);<br>
C21 = bem_Cij_lin(vol.bnd(2).pnt,vol.bnd(1).pnt,vol.bnd(1).tri, weight,defl(1));<br> tmp1 = C21/C11st;<br> <br> weight = (vol.cond(2)-vol.cond(3))/((vol.cond(1)+vol.cond(2))*2*pi);<br> C12 = bem_Cij_lin(vol.bnd(1).pnt,vol.bnd(2).pnt,vol.bnd(2).tri, weight,defl(2));<br>
weight = (vol.cond(2)-vol.cond(3))/((vol.cond(2)+vol.cond(3))*2*pi);<br> C22st = bem_Cii_lin(vol.bnd(2).tri,vol.bnd(2).pnt, weight,defl(2),vol.bnd(2).pnt4);<br> tmp2 = C12/C22st;<br> % ------------------------------------------------<br>
<br>where the matrix C11st contains three elements equal to NaN. Since C11st is then inverted, the result is a 'NaN' matrix.<br><br>I'll would very much appreciate your help<br>Thanks<br><font color="#888888">Gwenael</font></div>
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