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--></style></head><body lang="DE"><div class="WordSection1"><p class="MsoNormal"><span lang="EN-US" style="font-family:"Arial",sans-serif;color:black">Hello everybody,<o:p></o:p></span></p><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">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:<o:p></o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:red">Error using sb_calc_stiff (line 80)<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:red">Elements have wrong orientation or are degenerated<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:red"><o:p> </o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:red">Error in ft_headmodel_simbio (line 90)<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:red">headmodel.stiff = sb_calc_stiff(headmodel);<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:red"><o:p> </o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:red">Error in ft_prepare_headmodel (line 426)<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:red"> headmodel = ft_headmodel_simbio(geometry, 'conductivity', cfg.conductivity);<o:p></o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">Below is the code I am using to generate the mesh and the FEM model:<o:p></o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">cfg = [];<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">cfg.shift = 0.3;<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">cfg.tissue = {'gray','white','csf','skull','scalp'};<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">cfg.method = 'hexahedral';<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">mesh = ft_prepare_mesh(cfg,segmentedmri);<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">cfg = [];<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">cfg.method ='simbio';<o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; <o:p></o:p></span></pre><pre style="margin-left:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">FEMModel = ft_prepare_headmodel(cfg, mesh); <o:p></o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"> <o:p></o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">Has anyone experienced the same problem and know how to fix it?<o:p></o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">Thanks a lot,<o:p></o:p></span></pre><pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><pre><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></pre><p class="MsoNormal"><o:p> </o:p></p></div></body></html>