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<p class="MsoNormal"><span style="font-size:11.0pt">Ok, I will try that. Thank you so much for your help!!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Summer<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Oula Puonti <oulap@drcmr.dk><br>
<b>Date: </b>Friday, March 3, 2023 at 1:19 PM<br>
<b>To: </b>Frandsen, Summer Brianne <sfrandsen@bwh.harvard.edu>, discuss@simnibs.org <discuss@simnibs.org><br>
<b>Subject: </b>Re: [Simnibs-discuss] E-field brain matter options<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt"> External Email - Use Caution
<br>
<br>
Hi Summer,<br>
<br>
Aah, I see. Yeah at the moment there is no option to specify the<br>
tissues in the GUI. If you want to hardcode this for your specific<br>
simnibs version you should edit line 193 inside the sim_struct.py file.<br>
You can find the file inside <br>
<br>
<simnibs_installation_path>/simnibs/simulation<br>
<br>
and you should change the default tissues used, see<br>
<br>
<a href="https://secure-web.cisco.com/1LCPc7FEkoNfGimTxGj3_92cFiJfmIX7GDeoqM2rTORaTLrOLIFFfBEBf8C7AeKguZP_-L6TapgGGd1brWzOnpX16McHb0Ka6x-XyEeGqynQ22d9uDyK5z1-KAs2ZwUpDJML1fcRmc-pXHlwhnZEnM_PncuRRW-xUrVAhxk8AuVgxZSr6iIqtGq3X47g5PXPQt6PgzcP86StGVIVsOMfbLfOxp6DiWMs7VIDzbrY5EtaNGEKzgvq9EwR5BPnHiGUIYjgijQoO4oih_Wlu4igl0yUSuhxKH8YAUsKRic9ybucIyl1VwDvTC9reXc6VfmNz/https%3A%2F%2Fgithub.com%2Fsimnibs%2Fsimnibs%2Fblob%2Fmaster%2Fsimnibs%2Fsimulation%2Fsim_struct.py%23L193">https://secure-web.cisco.com/1LCPc7FEkoNfGimTxGj3_92cFiJfmIX7GDeoqM2rTORaTLrOLIFFfBEBf8C7AeKguZP_-L6TapgGGd1brWzOnpX16McHb0Ka6x-XyEeGqynQ22d9uDyK5z1-KAs2ZwUpDJML1fcRmc-pXHlwhnZEnM_PncuRRW-xUrVAhxk8AuVgxZSr6iIqtGq3X47g5PXPQt6PgzcP86StGVIVsOMfbLfOxp6DiWMs7VIDzbrY5EtaNGEKzgvq9EwR5BPnHiGUIYjgijQoO4oih_Wlu4igl0yUSuhxKH8YAUsKRic9ybucIyl1VwDvTC9reXc6VfmNz/https%3A%2F%2Fgithub.com%2Fsimnibs%2Fsimnibs%2Fblob%2Fmaster%2Fsimnibs%2Fsimulation%2Fsim_struct.py%23L193</a><br>
<br>
<br>
Best,<br>
Oula<br>
<br>
<br>
<br>
On Fri, 2023-03-03 at 15:18 +0000, Frandsen, Summer Brianne wrote:<br>
> Hi Oula. <br>
> <br>
> Sorry, I should have clarified! I’m talking about the nifti files<br>
> that are output when using the simnibs simulation GUI. The only files<br>
> I can get output are the ones with gray matter tissue.<br>
> <br>
> Thanks,<br>
> <br>
> Summer<br>
> <br>
> From:Oula Puonti <oulap@drcmr.dk><br>
> Date: Friday, March 3, 2023 at 8:33 AM<br>
> To: Frandsen, Summer Brianne <sfrandsen@bwh.harvard.edu>,<br>
> discuss@simnibs.org <discuss@simnibs.org><br>
> Subject: Re: [Simnibs-discuss] E-field brain matter options<br>
> External Email - Use Caution <br>
> <br>
> Hi Summer,<br>
> <br>
> Just to make sure: are we talking about gmsh or the simnibs<br>
> simulation<br>
> GUI?<br>
> <br>
> The simulated electric field is always calculated in all tissues so<br>
> you<br>
> can visualize the field in both the gray and white matter in gmsh.<br>
> The<br>
> surfaces and volumes between v4 and v3 look a bit different now, for<br>
> example the spinal cord is now fully white matter without a gray<br>
> matter<br>
> layer around it.<br>
> <br>
> In the simulation GUI the only brain surface you can visualize is the<br>
> gray matter surface.<br>
> <br>
> Best,<br>
> Oula<br>
> <br>
> <br>
> On Thu, 2023-03-02 at 20:34 +0000, Frandsen, Summer Brianne wrote:<br>
> > Hi,<br>
> > <br>
> > In previous SimNIBS versions (e.g. V 3.2.6), the default electric<br>
> > field modeling simulations included both grey and white matter when<br>
> > using the gui. However, the newest version appears to be use only<br>
> > grey matter. It seems like there is a way to change this option<br>
> > (e.g.<br>
> > including white matter) when scripting simulations, but I have been<br>
> > unable to find an option that allows me to do in the gui. Is there<br>
> > a<br>
> > way to do this in the gui?<br>
> > <br>
> > Thanks,<br>
> > <br>
> > Summer. Frandsen<br>
> > <br>
> > <br>
> > <br>
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