<div dir="ltr">Hi all,<div>following up on this email exchange, I created a pull request you can follow by adding a comment here:</div><div><a href="https://github.com/fieldtrip/fieldtrip/pull/1427">https://github.com/fieldtrip/fieldtrip/pull/1427</a><br></div><div>Best,</div><div>Maria Carla</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 27 May 2020 at 10:58, Johannes Vorwerk <<a href="mailto:j.vorw01@gmail.com">j.vorw01@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Hi Roberto,<div><br></div><div>having implemented the FieldTrip-Simbio pipeline and having worked on DBS myself, I would recommend you not to use a hexahedral mesh for this kind of simulations, since it is very hard to properly resolve the geometry of a DBS lead in a hexahedral mesh. Furthermore, the mesh should be especially refined around the DBS lead to achieve high numerical accuracies, which is only (easily) possible using tetrahedral meshes.</div><div><br></div><div>To achieve anisotropic conductivities in a tetrahedral mesh, I would recommend you to assign the anisotropy tensor of the voxel closest to the center of the tetrahedral element for each element. Additional interpolation of the tensors is quite tricky.</div><div><br></div><div>For DBS computations, I would also recommend you to take a look at LeadDBS (Horn, Andreas, et al. "Lead-DBS v2: Towards a comprehensive pipeline for deep brain stimulation imaging." Neuroimage 184 (2019): 293-316., <a href="http://lead-dbs.org" target="_blank">lead-dbs.org</a>), which relies on the same numerical background as FieldTrip-SimBio.</div><div><br></div><div>Best,</div><div><span style="white-space:pre-wrap"> </span>Johannes<br><div><br><blockquote type="cite"><div>On 27. May 2020, at 10:48, <<a href="mailto:roberto.garza@artorg.unibe.ch" target="_blank">roberto.garza@artorg.unibe.ch</a>> <<a href="mailto:roberto.garza@artorg.unibe.ch" target="_blank">roberto.garza@artorg.unibe.ch</a>> wrote:</div><br><div><div id="gmail-m_7281825899238850047divtagdefaultwrapper" dir="ltr" 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;text-decoration:none;font-size:12pt;font-family:Calibri,Helvetica,sans-serif"><div style="margin-top:0px;margin-bottom:0px">Good morning,</div><div style="margin-top:0px;margin-bottom:0px">I'm working in the DBS field and I'm using your library to obtain the headmodel. My aim is to include conductivity anisotropy in the computation of the electric field (by using the FieldTrip-SimBio pipeline). I have one conductivity matrix for each voxel in the image, so I built a hexahedral mesh to get a straightforward correspondence between an element and its conductivity. Now I need to integrate in the model the electrode as well: I have it in the form of a tetrahedral mesh. Is there a way to convert tetrahedral mesh to hexahedral? Or is there another way to integrate the two models that I'm not seeing?</div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px">Thank you for your time</div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px">Roberto Garza<br></div></div><span style="font-family:Helvetica;font-size:12px;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;text-decoration:none;float:none;display:inline">_______________________________________________</span><br style="font-family:Helvetica;font-size:12px;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;text-decoration:none"><span style="font-family:Helvetica;font-size:12px;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;text-decoration:none;float:none;display:inline">fieldtrip mailing list</span><br style="font-family:Helvetica;font-size:12px;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;text-decoration:none"><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family:Helvetica;font-size:12px;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" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="font-family:Helvetica;font-size:12px;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;text-decoration:none"><a href="https://doi.org/10.1371/journal.pcbi.1002202" style="font-family:Helvetica;font-size:12px;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" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a></div></blockquote></div><br></div></div>_______________________________________________<br>
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