<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">this question was already answered in this thread</div><div class=""><br class=""></div><div class=""><a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html" class="">http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html</a></div><div class=""><br class=""></div><div class="">If ft_volumereslice is not applied before the mesh generation, the afterwards applied transformation might flip the directions of the mesh, leading to the described error.</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Johannes</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">Am 06.04.2016 um 16:03 schrieb Carsten Wolters <<a href="mailto:carsten.wolters@uni-muenster.de" class="">carsten.wolters@uni-muenster.de</a>>:</div><br class="Apple-interchange-newline"><div class=""><div class="moz-cite-prefix" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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-stroke-width: 0px; background-color: rgb(255, 255, 255);">Dear Rajat,<br class=""><br class="">the element-node cards of SimBio-NeuroFEM need to follow certain orientations (see<span class="Apple-converted-space"> </span><a class="moz-txt-link-abbreviated" href="http://www.simbio.de/">www.simbio.de</a>).<br class=""><br class="">If you do not want to struggle with meshing/ordering, use the SimBio-VGRID mesher<span class="Apple-converted-space"> </span><br class=""><a class="moz-txt-link-freetext" href="http://vgrid.simbio.de/">http://vgrid.simbio.de/</a><br class="">that follows the required ordering of nodes. You might use this mesher to produce 1mm geometry-adapted FEM meshes<br class="">that show good overall performance, see<span class="Apple-converted-space"> </span><br class=""><a class="moz-txt-link-freetext" href="http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf">http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf</a><br class="">and<br class=""><a class="moz-txt-link-freetext" href="http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf">http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf</a><br class="">(latter was just accepted by NeuroImage).<span class="Apple-converted-space"> </span><br class=""><br class="">Best regards<br class=""> Carsten<br class=""><br class="">Am 06.04.2016 um 15:10 schrieb Rajat Thomas:<br class=""></div><blockquote cite="mid:1459948210999.59028@nin.knaw.nl" type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear all,<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Has anyone used the FEM approach to Headmodels using Simbio recently?<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">If so, I get this error:<br class=""></div><div class="">"Elements have wrong orientation or are degenerated"<br class=""></div><div class=""><br class=""></div><div class="">Any ideas?<br class=""></div><div class=""><br class=""></div><div class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">cfg = [];</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">cfg.method =<span class="s1">'simbio'</span>;</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; <span class="Apple-converted-space"> </span><span class="s2">% order follows mesh.tissyelabel</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">vol = ft_prepare_headmodel(cfg, mesh); <br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">And;<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div class="">disp(mesh)</div><div class=""> <span class="Apple-converted-space"> </span>hex: [545883x8 double]</div><div class=""> <span class="Apple-converted-space"> </span>pnt: [569722x3 double]</div><div class=""> labels: [545883x1 double]</div><div class=""> tissue: [545883x1 double]</div><div class=""> <span class="Apple-converted-space"> </span>tissuelabel: {'csf' 'gray' 'scalp' 'skull' 'white'}</div><div class=""> unit: 'mm'</div><div class=""> <span class="Apple-converted-space"> </span>cfg: [1x1 struct]<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div>Any help would be highly appreciated.<br class=""></div><div class=""><br class=""></div><div class="">Rajat<br class=""></div><div class=""><br class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div name="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; margin: 0px;" class=""><div name="divtagdefaultwrapper" style="font-family: Calibri; font-size: 12pt;" class=""><br class=""></div><div name="divtagdefaultwrapper" style="font-family: Calibri; font-size: 12pt;" class=""><br class=""></div><div name="divtagdefaultwrapper" style="font-family: Calibri;" class=""><font size="2" class="">Rajat Mani Thomas</font></div><div name="divtagdefaultwrapper" style="font-family: Calibri;" class=""><font size="2" class="">Social Brain Lab<br class=""></font><div class=""><font size="2" class="">Netherlands Institute for Neuroscience</font></div><div class=""><font size="2" class="">Amsterdam</font></div></div></div></div><br class=""><fieldset class="mimeAttachmentHeader"></fieldset><br class=""><pre wrap="" class="">_______________________________________________
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