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Dear Community, </div>
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I am analyzing resting state EEG data. We also have t1W images collected at another time. I would like to use the t1W images to create a head model for my EEG source analysis. </div>
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My current pipeline does not construct the head properly I get the error when computing volumen conduction:</div>
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Error using ft_headmodel_bemcp (line 127)<br class="ContentPasted2">
vertex 467 of surface 2 is outside surface 3<br>
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The pipeline was taken from the Fieldtrip turorial websites. See below. See also attached for MRI and segmented visualizations. I have tried chagning <span style="background-color:rgb(255, 255, 255);display:inline !important" class="ContentPasted1 ContentPasted4">cfg.scalpthreshold,
but have not landed on a desirable outcome. I have also used ft_volumebiascorrect and the scalp is not calculated correctly. Is there another strategy that I can use to calculate the scalp correctly?</span></div>
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%Interactive Search of Fids
<div class="ContentPasted0">cfg = [];</div>
<div class="ContentPasted0">cfg.method = 'interactive'</div>
<div class="ContentPasted0">cfg.coordsys = 'ctf'; % the desired coordinate system</div>
<div class="ContentPasted0">mri_realigned = ft_volumerealign(cfg, mri)</div>
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<div class="ContentPasted0">%Cut image</div>
<div class="ContentPasted0">cfg = [];</div>
<div class="ContentPasted0">cfg.method = 'linear';</div>
<div class="ContentPasted0">mri_resliced = ft_volumereslice(cfg, mri_realigned);</div>
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<div class="ContentPasted0">%Segment to areas</div>
<div class="ContentPasted0">cfg = [];</div>
<div class="ContentPasted0">cfg.output = {'brain', 'skull', 'scalp'};</div>
<div class="ContentPasted0">%cfg.scalpthreshold = 0.1;</div>
<div class="ContentPasted0">%cfg.scalpsmooth = 'no';</div>
<div class="ContentPasted0">segmentedmri = ft_volumesegment(cfg, mri_resliced);</div>
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<div class="ContentPasted0">disp(segmentedmri)</div>
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<div class="ContentPasted0">%Visualize the segmentation result</div>
<div class="ContentPasted0">segmentedmri_indexed = ft_checkdata(segmentedmri, 'segmentationstyle', 'indexed')</div>
<div class="ContentPasted0">segmentedmri_indexed.anatomy = mri_resliced.anatomy;</div>
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<div class="ContentPasted0">cfg = [];</div>
<div class="ContentPasted0">cfg.method = 'ortho';</div>
<div class="ContentPasted0">cfg.anaparameter = 'anatomy';</div>
<div class="ContentPasted0">cfg.funparameter = 'tissue';</div>
<div class="ContentPasted0">cfg.funcolormap = [</div>
<div class="ContentPasted0"> 0 0 0</div>
<div class="ContentPasted0"> 1 0 0</div>
<div class="ContentPasted0"> 0 1 0</div>
<div class="ContentPasted0"> 0 0 1</div>
<div class="ContentPasted0"> ];</div>
<div class="ContentPasted0">ft_sourceplot(cfg, segmentedmri_indexed)</div>
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<div class="ContentPasted0">%Create Mesh</div>
<div class="ContentPasted0">cfg = [];</div>
<div class="ContentPasted0">cfg.tissue = {'brain', 'skull', 'scalp'};</div>
<div class="ContentPasted0">cfg.numvertices = [3000 2000 1000];</div>
<div class="ContentPasted0">mesh = ft_prepare_mesh(cfg, segmentedmri);</div>
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<div class="ContentPasted0">%Plot Mesh</div>
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<div class="ContentPasted0">figure</div>
<div class="ContentPasted0">ft_plot_mesh(mesh(1), 'facecolor', 'none'); % brain</div>
<div class="ContentPasted0">view([0 -1 0]); % from the right side</div>
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<div class="ContentPasted0">figure</div>
<div class="ContentPasted0">ft_plot_mesh(mesh(2), 'facecolor', 'none'); % skull</div>
<div class="ContentPasted0">view([0 -1 0]); % from the right side</div>
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<div class="ContentPasted0">figure</div>
<div class="ContentPasted0">ft_plot_mesh(mesh(3), 'facecolor', 'none'); % scalp</div>
<div class="ContentPasted0">view([0 -1 0]); % from the right side</div>
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<div class="ContentPasted0">figure</div>
<div class="ContentPasted0">ft_plot_mesh(mesh(1), 'facecolor','r', 'facealpha', 1.0, 'edgecolor', 'k', 'edgealpha', 1);</div>
<div class="ContentPasted0">hold on</div>
<div class="ContentPasted0">ft_plot_mesh(mesh(2), 'facecolor','g', 'facealpha', 0.4, 'edgecolor', 'k', 'edgealpha', 0.1);</div>
<div class="ContentPasted0">hold on</div>
ft_plot_mesh(mesh(3), 'facecolor','b', 'facealpha', 0.4, 'edgecolor', 'k', 'edgealpha', 0.1);<br>
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% Create a volume conduction model
<div class="ContentPasted3">cfg = [];</div>
<div class="ContentPasted3">cfg.method = 'bemcp'; % You can also specify 'openmeeg', 'bemcp', or another method</div>
<div class="ContentPasted3">headmodel = ft_prepare_headmodel(cfg, mesh);</div>
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