<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><font size="2" class="">Hi Oula,</font><div class=""><font size="2" class=""><br class=""></font></div><div class=""><font size="2" class="">I just wanted to clarify: the coordinate (x,y,z) defines the location of the electrode in the space, therefore, the z axis does not determine the distance of the electrode to the skin. As it states in the website the <span lang="TR" style="text-indent: -18pt;" class="">c</span><span lang="EN-US" style="text-indent: -18pt; background-color: white;" class="">oordinates do not need to be exactly in the skin
surface, as SimNIBS automatically finds the closest point in the skin surface. Therefore, whatever I give as the coordinates of the electrode, SimNIBS will place my electrodes on to the closest points to the skin surface.</span></font></div><div style="text-indent: -24px;" class=""><font size="2" class=""> Otherwise, how can I state in the script or in the gui that I would like to position the electrodes on to the skin? There is a skin distance parameter for the TMS electrodes, however, I could not see that for tDCS electrodes.</font></div><div style="text-indent: -24px;" class=""><font size="2" class=""><br class=""></font></div><div style="text-indent: -24px;" class=""><font size="2" class=""> Thank you for your help in advance.</font></div><div style="text-indent: -24px;" class=""><font size="2" class=""> Best wishes,</font></div><div style="text-indent: -24px;" class=""><font size="2" class=""> Gülce</font></div><div class=""><div style="text-indent: -24px;" class=""><br class=""></div><!--EndFragment--><div><br class=""><blockquote type="cite" class=""><div class="">On 27 Jan 2023, at 14:55, Oula Puonti <<a href="mailto:oulap@drcmr.dk" class="">oulap@drcmr.dk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Gülce,<br class=""><br class="">You can just take the center coordinate (x,y,z) for the electrode from<br class="">the MRI, put that in the GUI (or a script), and project the coordinate<br class="">to the skin surface. This will keep the x and y coordinates (more or<br class="">less) the same but set the z so that the position is on the skin. After<br class="">that, when you define the electrode shape, just add a 2mm gel layer and<br class="">that should be it.<br class=""><br class="">Best,<br class="">Oula<br class=""><br class=""><br class="">On Wed, 2023-01-25 at 14:15 +0100, Gülce Lale wrote:<br class=""><blockquote type="cite" class="">Dear Oula,<br class="">Thank you for the help. We were able to label electrode gel as<br class="">background in the segmentation. However, when deriving our electrode<br class="">center coordinates, we still define the top of the electrode gel. We<br class="">know that we apply 2mm of electrode gel on top of the electrodes.<br class="">Thus, the coordinates acquired from the MRI image should be 2mm<br class="">below, so that they are at the actual skull height. <br class="">How do we convert length measures such as 2mm into world coordinates<br class="">which SimNIBS uses? And, can I find information on this on the<br class="">website?<br class="">Thank you for your time.<br class="">Best wishes,<br class="">Gülce<br class=""><br class=""><blockquote type="cite" class="">On 20 Jan 2023, at 19:11, Oula Puonti <<a href="mailto:oulap@drcmr.dk" class="">oulap@drcmr.dk</a>> wrote:<br class=""><br class="">Hi Gülce,<br class=""><br class="">You should leave them out, i.e., label them as background. SimNIBS<br class="">places the electrodes automatically during the simulation, so you<br class="">don't<br class="">need to add them to the headmodel yourself.<br class=""><br class="">You can record the center coordinate of the electrodes from the MRI<br class="">scans and pass that to the simulation so that the electrodes are<br class="">placed<br class="">correctly.<br class=""><br class="">Best,<br class="">Oula<br class=""><br class=""><br class="">On Fri, 2023-01-20 at 17:25 +0100, Gülce Lale wrote:<br class=""><blockquote type="cite" class="">Hi Oula,<br class=""><br class="">Thank you very much for your response, I will try it with charm<br class="">and<br class="">SimNIBS4.<br class="">I would like to clarify something and ask for your opinion. What<br class="">tissue the electrodes should be segmented as? Should they be left<br class="">out<br class="">of the segmentation? Or be segmented as one of the other 15<br class="">tissues?<br class=""><br class="">Thank you for your help in advance.<br class="">Best wishes,<br class="">Gülce<br class=""><br class=""><blockquote type="cite" class="">On 17 Jan 2023, at 19:54, Oula Puonti <<a href="mailto:oulap@drcmr.dk" class="">oulap@drcmr.dk</a>> wrote:<br class=""><br class="">Hi Gülce,<br class=""><br class="">I would consider this a segmentation error. You might want to<br class="">try<br class="">the<br class="">new segmentation method (charm) included in simnibs version 4.<br class="">In<br class="">my<br class="">experience it does a bit better job on ignoring the electrodes<br class="">in<br class="">the<br class="">type of MRI data you have.<br class=""><br class="">The other option is that you edit the skin masks, which are<br class="">inside<br class="">the<br class="">MASK_prep folder, manually and then re-run the surface and<br class="">volume<br class="">masking steps.<br class=""><br class="">The manual editing process was made easier in the new version,<br class="">see<br class="">here: <br class=""><br class=""><a href="https://simnibs.github.io/simnibs/build/html/tutorial/advanced/fix_headmodel.html" class="">https://simnibs.github.io/simnibs/build/html/tutorial/advanced/fix_headmodel.html</a><br class=""><br class="">so you might want to consider using SimNIBS4 in any case.<br class=""><br class="">Best,<br class="">Oula<br class=""><br class=""><br class="">On Tue, 2023-01-17 at 15:50 +0100, Gülce Lale wrote:<br class=""><blockquote type="cite" class="">Dear SimNIBS Team,<br class="">We conduct post-hoc modelling for each subject using T1 and<br class="">T2<br class="">images<br class="">acquired while the participant was in the scanner with the<br class="">tDCS<br class="">electrodes attached. Here SimNIBS headreco images the 2mm<br class="">layer<br class="">of<br class="">electrode paste and includes in in the head mesh but segments<br class="">it<br class="">as<br class="">skin (see attached images).<br class="">According to SimNIBS skin conductance is 0.465 s/m and the<br class="">electrode<br class="">material conductivity is 29.4 s/m. One would expect the Ten20<br class="">Electrode paste which is applied with a 2mm thickness between<br class="">the<br class="">electrode and skin to have a different measure. However,<br class="">since it<br class="">is<br class="">being considered and modelled as skin this could results in<br class="">deviations in the electric field modelling.<br class="">How do we account/solve this?<br class="">Could we model the electrodes 2mm below the head surface,<br class="">knowing<br class="">that the outer 2mm thickness of the skin are actually due to<br class="">the<br class="">paste? Thus, modelling the electrodes on the “actual” skin<br class="">outer<br class="">layer (and not on top of the paste). SimNIBS then allows us<br class="">to<br class="">specify past + electrode thickness. Where we assume SimNIBS<br class="">calculates a different conductivity measure for both.<br class="">Is there an alternative solution to best account for the<br class="">change<br class="">of<br class="">conductance?<br class="">Thank you for your help in advance.<br class="">Best wishes,<br class="">Gülce <br class=""><br class="">Gülce Lale<br class="">MSc Neurosciences<br class=""><br class="">_______________________________________________<br class="">Simnibs-discuss mailing list<br class="">Simnibs-discuss@drcmr.dk<br class="">https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss<br class=""></blockquote></blockquote><br class=""></blockquote><br class=""></blockquote><br class=""></blockquote><br class=""></div></div></blockquote></div><br class=""></div></body></html>