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Hi Edward,
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<div class="">Is there a particular reason why you reslice the image? As long as it’s not anisotropic there should no specific reason to do so. I ask because it seems that the displayed meshes are cut off at the back of the head, which may suggest too small
a bounding box at the back of the head.</div>
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<div class="">Best wishes,</div>
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<div class="">Jan-Mathijs<br class="">
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<div class="">On 21 Mar 2023, at 23:29, Edward Lannon via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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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 class="">
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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 class="ContentPasted1 ContentPasted4" style="background-color: rgb(255, 255, 255); display: inline !important;">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>
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<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 class="">
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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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<span id="cid:E9F67C80-A978-47E9-AD4D-33EEF196F032"><Brain.jpg></span><span id="cid:1AC6C1F9-FD95-48EA-BED5-A8A23BFBE51B"><Skull.jpg></span><span id="cid:B602332C-36F7-4957-9390-FBD6E4C8CFDF"><Scalp.jpg></span><span id="cid:A1D1AEE5-1B0D-4ABE-BFB3-64B16B2F8906"><HeadModel.jpg></span><span id="cid:80C3F3A0-0B36-45E4-A710-39C46AC9A92F"><Original_MRI.jpg></span><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!5jJcbM2emFh0ZA5a3cYSmgT1pVUo_Jdc1EhFm7GzBCUQpHA6HcGvPjYnx5aZlkSVtkFzEvdVmuSfhIB1KPBHm051SCEs-e8v63P48w$" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!5jJcbM2emFh0ZA5a3cYSmgT1pVUo_Jdc1EhFm7GzBCUQpHA6HcGvPjYnx5aZlkSVtkFzEvdVmuSfhIB1KPBHm051SCEs-e8v63P48w$</a><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span></div>
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