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<p>Dear all,</p>
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<p>I think I have found an inconsistency in the way Fieldtrip handles the building of a FEM forward solution. <span style="font-size: 12pt;">I am following the procedure described in </span><span style="font-size: 12pt;">Vorwerk, Oostenveld et al., </span><span style="font-size: 12pt;">The </span><span style="font-size: 12pt;">FieldTrip-SimBio
pipeline for EEG forward solutions. Biomed Eng Online. 2018 </span><span style="font-size: 12pt;">(</span><a href="https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-018-0463-y" class="OWAAutoLink" id="LPlnk762959" previewremoved="true" style="font-size: 12pt;">https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-018-0463-y</a><span style="font-size: 12pt;">).
This procedure suggests to build the forward solution by calling the following Fieldtrip functions:</span></p>
<p>ft_read_mri</p>
<p>ft_volumerealign</p>
<p>ft_volumereslice</p>
<p>ft_volumesegment</p>
<p>ft_prepare_mesh</p>
<p>ft_prepare_headmodel</p>
<p> ft_read_header (to get electrode data)</p>
<p> ft_electroderealign</p>
<p>ft_prepare_vol_sens</p>
<p>ft_prepare_sourcemodel</p>
<p>ft_prepare_leadfield</p>
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<p>My issue is the following: the FieldTrip-SimBio pipeline explicitly calls ft_prepare_vol_sens, which takes very long to execute (over 6 hours in the case of the published paper, which used about 80 electrodes). However, ft_prepare_leadfield later calls (line
165) prepare_headmodel, which <span style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">
itself </span>calls (line 113) ft_prepare_vol_sens again, with the same parameters as far as I can tell (and again taking ages to run).</p>
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<p>Is this redundancy intended? If not, can it be circumvented?</p>
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<p>Thank you in advance,</p>
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<p>Pierre</p>
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<div class="PlainText">Pierre Mégevand, MD, PhD<br>
Senior research associate, Dept. of basic neurosciences</div>
<div class="PlainText"><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">F</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">aculty of medicine</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">, </span>University
of Geneva, Switzerland<br>
T. +41 76 693 65 22 | pierre.megevand@unige.ch</div>
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