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Dear Martin,
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<div class="">I would assume that the order of the tissuelabel is what’s in the data, i.e. the hexahedral elements that get a value of ‘1’ in your data example will be the csf compartment. I would visualize the segmentation to verify this. Not sure whether
ft_sourceplot is capable of this out of the box, but I would assume that the ’tissue’ field should be reshapeable into a 3D volume, and visualized along with the anatomical image.</div>
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<div class="">Anyway, I think that the order of the conductivity values in the cfg should be the same as the order of the tissuelabel in the mesh. The low-level simbio code does not do an extra check on this. Perhaps the simbio folks can chime in here, because
they know the relevant code better than I do.</div>
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</div>
<div class="">I think that it might be worthwile to consider building in an extra sanity check at a higher level in the code, where the cfg into ft_prepare_headmodel also informs the code about which conductivity value is to be associated with a particular
tissue compartment. @the simbio/duneuro folks: what do you think?</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs <br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 7 Apr 2022, at 17:23, Martin Schaefer via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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Dear mailinglist,</div>
<div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<br class="">
</div>
<div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
I noticed that the function ft_prepare_mesh seems to change the order of the<span style="font-size: 11pt; line-height: 15.693333625793457px; font-family: Calibri, sans-serif;" class=""> segmentation layers to alphabetical, rather than keeping the order chosen
during ft_volumesegment.</span></div>
<div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<span style="font-size: 11pt; line-height: 15.693333625793457px; font-family: Calibri, sans-serif;" class="">This seems like it could potentially lead to a <span style="font-size: 11pt; line-height: 15.693333625793457px; font-family: Calibri, sans-serif;" class="">to
a mismatch with the conductivity values chosen during ft_prepare_headmodel, which uses the layer order from ft_prepare_mesh.</span></span></div>
<div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<span style="font-size: 11pt; line-height: 15.693333625793457px; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt; line-height: 15.693333625793457px; font-family: Calibri, sans-serif;" class=""><br class="">
</span></span></div>
<div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<span style="font-size: 11pt; line-height: 15.693333625793457px; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt; line-height: 15.693333625793457px; font-family: Calibri, sans-serif;" class="">For example, I run </span></span></div>
<div 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="">
<blockquote itemscope="" itemtype="https://schemas.microsoft.com/QuotedText" style="border-left-width: 3px; border-left-style: solid; border-color: rgb(200, 200, 200); padding-left: 1ex; margin-left: 0.8ex;" class="">
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cfg = [];
<div class="elementToProof">cfg.output = {'gray','white','csf','skull','scalp'};</div>
</div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
mri_segmented = ft_volumesegment(cfg, mri_resliced);<br class="">
</div>
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<div class="elementToProof" style=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">followed by </span><br class="">
</div>
<blockquote itemscope="" itemtype="https://schemas.microsoft.com/QuotedText" style="border-left-width: 3px; border-left-style: solid; border-color: rgb(200, 200, 200); padding-left: 1ex; margin-left: 0.8ex;" class="">
<div class="elementToProof" style=""><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">cfg = [];
<div class="elementToProof">cfg.shift = 0.3; </div>
<div class="elementToProof">cfg.method = 'hexahedral'; </div>
</span></div>
<div class="elementToProof" style=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">mesh = ft_prepare_mesh(cfg,mri_segmented);<br class="">
</span></div>
</blockquote>
<div class="elementToProof" style=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">When I then look at mesh.tissuelabel the order has changed to: {'csf'} {'gray'} {'scalp'}
{'skull'} {'white'}</span><span style="background-color: rgb(255, 255, 255);" class=""><br class="">
</span></div>
<div class="elementToProof" style=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class="">
</span></div>
<div class="elementToProof" style=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">And if I continue to run </span></div>
<blockquote itemscope="" itemtype="https://schemas.microsoft.com/QuotedText" style="border-left-width: 3px; border-left-style: solid; border-color: rgb(200, 200, 200); padding-left: 1ex; margin-left: 0.8ex;" class="">
<div class="elementToProof" style=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">cfg = [];</span></div>
<div class="elementToProof" style=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">
<div class="">cfg.method = 'simbio';</div>
<div class="">cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % {'gray' 'white' 'csf' 'skull' 'scalp'}</div>
<div class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">headmodel_eeg = ft_prepare_headmodel(cfg, mesh_fem);</span><br class="">
</div>
</span></div>
</blockquote>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">headmodel_eeg.tissuelabel has the same order as the mesh: <span style="background-color: rgb(255, 255, 255); display: inline !important;" class=""><span class=""> </span>{'csf'}
{'gray'} {'scalp'} {'skull'} {'white'}</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class="">And I assume this means the conductivity values are mismatched.</span></span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class="">
</span></span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class="">Can someone check this?</span></span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class="">
</span></span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class="">I use the fieldtrip version from 1<span class=""><sup class="">st</sup> </span>of
April 2022.</span></span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class="">
</span></span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class="">Best regards,</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class="">Martin</span></span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="background-color: rgb(255, 255, 255); display: inline !important;" class=""><br class="">
</span></span></div>
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