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<p class="MsoNormal">Dear All,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none">I started with fieldTrip recently and I am trying to create a BEM headmodel using the mri data (<span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">standard_mri.mat</span>) available on the
website. I use the following code<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">load standard_mri.mat</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">mri_orig=mri;<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">% Realign the data to the CTF system<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.method = 'interactive';<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">% use n,l,r fudicials</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">mri_realign = ft_volumerealign(cfg, mri_orig);</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.resolution = 1; % mm</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.dim = mri_orig.dim;</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">mri_reslice = ft_volumereslice(cfg, mri_realign);</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black">%%
</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">Segmenting the data<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.output= {'scalp','skull','brain'};</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.coordinates = 'ctf';
</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.keepintermediate = 'no';</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">[mri_segment] = ft_volumesegment(cfg, mri_reslice);
</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">mri_combine = mri_reslice;</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">mri_combine.seg = mri_segment.scalp + 3*mri_segment.skull + 6*mri_segment.brain;</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">mri_combine.mask = (mri_combine.seg)>0;<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">%% Plot data<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.interactive = 'no';</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.method='slice';
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.funparameter = 'seg';</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.funcolormap = 'jet';</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.funcolorlim = [0 7];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.opacitylim = [0 1.5];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.maskparameter = 'mask';</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">figure , ft_sourceplot(cfg,mri_combine);</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">%% Generating the mesh<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg=[];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.tissue=[1 2 3];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.numvertices=[5000 3000 800];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> cfg.sourceunits=mri_segment.unit;</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> scalp=(mri_segment.scalp)&~(mri_segment.skull | mri_segment.brain);</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> skull=2*(mri_segment.skull);</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> brain=3*(mri_segment.brain);</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> mri_segment.seg= scalp+skull+brain;</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> bnd = ft_prepare_mesh(cfg, mri_segment);</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black">%</span><span style="font-size:10.0pt;font-family:"Courier New";color:black">% View meshes a transparent plot<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">figure (2)</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">tr1=TriRep(bnd(1).tri,bnd(1).pnt(:,1),bnd(1).pnt(:,2),bnd(1).pnt(:,3));</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">tr2=TriRep(bnd(2).tri,bnd(2).pnt(:,1),bnd(2).pnt(:,2),bnd(2).pnt(:,3));</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">tr3=TriRep(bnd(3).tri,bnd(3).pnt(:,1),bnd(3).pnt(:,2),bnd(3).pnt(:,3));</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> trisurf(tr1,'facealpha',0.1); hold on</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> trisurf(tr2,'facealpha',0.2); hold on</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> trisurf(tr3)</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">%% BEM Computation-calculating the related electromagnetic model</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">Cskin_surface= 0.33; %scalp</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">Couter_skull_surface=0.0042; %skull</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">Cinner_skull_surface=0.33; %brain</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">vol=[];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">for i=1:3</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">vol.bnd(i).tri=bnd(i).tri;</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">vol.bnd(i).pnt=bnd(i).pnt;</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">end</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">vol.cond=[Cskin_surface Couter_skull_surface Cinner_skull_surface];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg=[];</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.method = 'openmeeg';</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">vol = ft_prepare_headmodel(cfg, vol);</span><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:12.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none">When I run the code at the stage of generating the headmodel with
<span style="font-size:10.0pt;font-family:"Courier New";color:black">ft_prepare_headmodel,
</span><span style="color:black">I get an error as;</span><o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none">??? Error using ==> surface_nesting at 24<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none">the compartment nesting cannot be determined<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none">Error in ==> ft_headmodel_bem_openmeeg at 96<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none">order = surface_nesting(vol.bnd, 'insidefirst');<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none">With the limited experience with fieldTrip and headmodels I assume that this is because the meshes are overlapping.<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none">I would really appreciate any guidance and any suggestions given to make this work.<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none">Many thanks in advance.<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none">Kind regards<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none">Imali<o:p></o:p></p>
<p class="MsoNormal" style="text-autospace:none"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU">Imali Thanuja Hettiarachchi<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU">PhD Candidate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU">Centre for Intelligent Systems research<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU">Deakin University,
</span><span style="font-size:10.0pt;font-family:"Times New Roman","serif";color:black;mso-fareast-language:EN-AU">Geelong 3217, Australia.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Times New Roman","serif";color:black;mso-fareast-language:EN-AU">Email:
<a href="mailto:ith@deakin.edu.au">ith@deakin.edu.au</a><br>
</span><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU"><a href="http://www.deakin.edu.au/cisr">www.deakin.edu.au/cisr</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black;mso-fareast-language:EN-AU"><img border="0" width="70" height="73" id="Picture_x0020_1" src="cid:image001.jpg@01CD431E.D3C538D0" alt="Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD@deakin.edu.au"></span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:EN-AU"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:EN-AU"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="mso-fareast-language:EN-AU"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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