[FieldTrip] error in FEM model

[Yuranny Cabral-Calderin]

Hello everybody,

I am using Fieldtrip to generate FEM head models. I segment my MRI data outside of MATLAB (using the Simnibs pipeline + manual corrections in SEG3D). I import my segmentation in MATLAB and use ft_prepare_mesh to generate the hexahedral mesh. This seems to work fine. However, when I pass the resulting mesh to the ft_prepare_headmodel function, I get the following error:


Error using sb_calc_stiff (line 80)
Elements have wrong orientation or are degenerated

Error in ft_headmodel_simbio (line 90)
headmodel.stiff = sb_calc_stiff(headmodel);

Error in ft_prepare_headmodel (line 426)
    headmodel = ft_headmodel_simbio(geometry, 'conductivity', cfg.conductivity);



Below is the code I am using to generate the mesh and the FEM model:

cfg        = [];
cfg.shift  = 0.3;
cfg.tissue = {'gray','white','csf','skull','scalp'};
cfg.method = 'hexahedral';
mesh       = ft_prepare_mesh(cfg,segmentedmri);


cfg              = [];
cfg.method       ='simbio';
cfg.conductivity = [0.33 0.14 1.79 0.01 0.43];   
FEMModel         = ft_prepare_headmodel(cfg, mesh);   


 
Has anyone experienced the same problem and know how to fix it?

Thanks a lot,



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https://doi.org/10.1371/journal.pcbi.1002202