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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
Dear mailinglist,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
I noticed that the function ft_prepare_mesh seems to change the order of the<span style="font-size:11.0pt;line-height:107%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA"> segmentation
layers to alphabetical, rather than keeping the order chosen during ft_volumesegment.
</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
<span style="font-size:11.0pt;line-height:107%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA">This
seems like it could potentially lead to a <span style="font-size:11.0pt;line-height:107%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA">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 style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
<span style="font-size:11.0pt;line-height:107%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA"><span style="font-size:11.0pt;line-height:107%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA"><br>
</span></span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
<span style="font-size:11.0pt;line-height:107%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA"><span style="font-size:11.0pt;line-height:107%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA">For
example, I run </span></span></div>
<div>
<blockquote itemscope="" itemtype="https://schemas.microsoft.com/QuotedText" style="border-left: 3px solid rgb(200, 200, 200); border-top-color: rgb(200, 200, 200); border-right-color: rgb(200, 200, 200); border-bottom-color: rgb(200, 200, 200); padding-left: 1ex; margin-left: 0.8ex;">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
cfg = [];
<div class="elementToProof">cfg.output = {'gray','white','csf','skull','scalp'};</div>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
mri_segmented = ft_volumesegment(cfg, mri_resliced);<br>
</div>
</blockquote>
<div style="color: rgb(0, 0, 0);" class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">followed by </span><br>
</div>
<blockquote itemscope="" itemtype="https://schemas.microsoft.com/QuotedText" style="border-left: 3px solid rgb(200, 200, 200); border-top-color: rgb(200, 200, 200); border-right-color: rgb(200, 200, 200); border-bottom-color: rgb(200, 200, 200); padding-left: 1ex; margin-left: 0.8ex;">
<div style="color: rgb(0, 0, 0);" class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">cfg = [];
<div class="elementToProof">cfg.shift = 0.3; </div>
<div class="elementToProof">cfg.method = 'hexahedral'; </div>
</span></div>
<div style="color: rgb(0, 0, 0);" class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">mesh = ft_prepare_mesh(cfg,mri_segmented);<br>
</span></div>
</blockquote>
<div style="color: rgb(0, 0, 0);" class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">When I then look at mesh.tissuelabel the order has changed
to: {'csf'} {'gray'} {'scalp'} {'skull'} {'white'}</span><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
</span></div>
<div style="color: rgb(0, 0, 0);" class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
</span></div>
<div style="color: rgb(0, 0, 0);" class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">And if I continue to run </span></div>
<blockquote itemscope="" itemtype="https://schemas.microsoft.com/QuotedText" style="border-left: 3px solid rgb(200, 200, 200); border-top-color: rgb(200, 200, 200); border-right-color: rgb(200, 200, 200); border-bottom-color: rgb(200, 200, 200); padding-left: 1ex; margin-left: 0.8ex;">
<div style="color: rgb(0, 0, 0);" class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">cfg = [];</span></div>
<div style="color: rgb(0, 0, 0);" class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<div>cfg.method = 'simbio';</div>
<div>cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % {'gray' 'white' 'csf' 'skull' 'scalp'}</div>
<div><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">headmodel_eeg = ft_prepare_headmodel(cfg, mesh_fem);</span><br>
</div>
</span></div>
</blockquote>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">headmodel_eeg.tissuelabel has the same order as the mesh: <span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;"><span> </span>{'csf'}
{'gray'} {'scalp'} {'skull'} {'white'}</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">And I assume this means the conductivity values are mismatched.</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;"><br>
</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">Can someone check this?</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;"><br>
</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">I use the fieldtrip version from 1<span><sup>st</sup> </span>of April 2022.</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;"><br>
</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">Best regards,</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">Martin</span></span></div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;"><br>
</span></span></div>
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<font color="#333333" size="1" style=""><span lang="en-US" style="margin:0px"><span style="color: rgb(118, 113, 113); font-family: Calibri, sans-serif; font-size: 12px; text-align: left; background-color: rgb(255, 255, 255); display: inline !important;">------------</span><br>
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<p style="color: rgb(32, 31, 30); font-family: Tahoma; font-size: 13px; text-align: start; background-color: rgb(255, 255, 255); margin-top: 0px; margin-bottom: 0px;">
<font color="#333333" size="1" style=""><span lang="en-US" style="margin:0px"><b>Martin Schaefer | </b></span></font><span style="font-family:Tahoma; font-size:x-small">PhD Student</span></p>
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<font color="#333333" size="1" style=""><span style="font-family: Tahoma; font-size: x-small; background-color: rgb(255, 255, 255); display: inline !important;"><a href="https://www.perceptionlab.se/">https://www.perceptionlab.se/</a><br>
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<font color="#333333" size="1" style="">Department of Clinical Neuroscience (CNS), K8</font></p>
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<font color="#333333" size="1" style="">Karolinska Institutet | 17 177 Stockholm | Nobels väg 9</font></p>
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<span lang="en-US" style="margin:0px"><font color="gray" size="1" style=""><a href="mailto:artin.arshamian@ki.se" target="_blank" rel="noopener noreferrer" style="margin:0px">martin.schaefer@ki.se</a></font></span></p>
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<span lang="en-US" style="margin:0px"><font color="gray" size="1" style="">______________________________________<br>
Karolinska Institutet – a Medical University</font></span></p>
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