<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:10.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="EN-US" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt">Hi Oula. <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">Sorry, I should have clarified! I’m talking about the nifti files that are output when using the simnibs simulation GUI. The only files I can get output are the ones with gray matter tissue.<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">Thanks,<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 8:33 AM<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>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt"> External Email - Use Caution
<br>
<br>
Hi Summer,<br>
<br>
Just to make sure: are we talking about gmsh or the simnibs simulation<br>
GUI?<br>
<br>
The simulated electric field is always calculated in all tissues so you<br>
can visualize the field in both the gray and white matter in gmsh. 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 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 (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 a<br>
> way to do this in the gui?<br>
> <br>
> Thanks,<br>
> <br>
> Summer. Frandsen<br>
> <br>
> <br>
> <br>
> The information in this e-mail is intended only for the person to<br>
> whom it is addressed. If you believe this e-mail was sent to you in<br>
> error and the e-mail contains patient information, please contact the<br>
> Mass General Brigham Compliance HelpLine at<br>
> <a href="https://secure-web.cisco.com/1tS_WezwgoKpVHOsYs5udX7LV6ThVF8UnIsBSY4Yte9wbjsv-35ZzmL--UFMaFDsqbsnneQPHQJAs08ICtjPXU4t5b0RHSflEV271oIZLg7XQUdL2uyHgUiDMIyeA5Wme2C8OaR4eUfGm74JxhiS9oiyB3DI5Ujz1-UQ390Gxc8l0RMvof6u5YGGWIbWcwMZ4KcWCGAc8T1IJhkqBkw7WTuyXmsyLfS7SzSernkDC7KchSsp9e9zHwOH32y_lXO7bFk7PzEdwYMc233gceIL9zIDAjxIWCNKooGE9D8paLtUkAn1DHmlBFzAozxcUO79e/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline">
https://secure-web.cisco.com/1tS_WezwgoKpVHOsYs5udX7LV6ThVF8UnIsBSY4Yte9wbjsv-35ZzmL--UFMaFDsqbsnneQPHQJAs08ICtjPXU4t5b0RHSflEV271oIZLg7XQUdL2uyHgUiDMIyeA5Wme2C8OaR4eUfGm74JxhiS9oiyB3DI5Ujz1-UQ390Gxc8l0RMvof6u5YGGWIbWcwMZ4KcWCGAc8T1IJhkqBkw7WTuyXmsyLfS7SzSernkDC7KchSsp9e9zHwOH32y_lXO7bFk7PzEdwYMc233gceIL9zIDAjxIWCNKooGE9D8paLtUkAn1DHmlBFzAozxcUO79e/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline</a>
.<br>
> <br>
> Please note that this e-mail is not secure (encrypted). If you do<br>
> not wish to continue communication over unencrypted e-mail, please<br>
> notify the sender of this message immediately. Continuing to send or<br>
> respond to e-mail after receiving this message means you understand<br>
> and accept this risk and wish to continue to communicate over<br>
> unencrypted e-mail. <br>
> _______________________________________________<br>
> Simnibs-discuss mailing list<br>
> Simnibs-discuss@drcmr.dk<br>
> <a href="https://secure-web.cisco.com/1Mwi4oAKB2067fFkbaEJ3fhrzJKQDQrVgSXNK9STlqMnyBAi2L_meEk7y8CCdAj5u2hdEQKzxx03w9A1Zus9SDz97WSxDJz4W3cm55PeSt5_wFdxhnz7eOXeSKpX8e2pt_pdheNTMPh-LZP4s9RDbb7EDzljFPeg9v12LJ5z4sY9-zqMQ2dWPJVHtI3KzqJvgF9H_iw6N4vdnfZmLeISOoGZhBSbPAlA1gTOi84R-av18O0M3QEPqCRnLGWfJOAS3IpGPoiS2Sglu6B7dtOITlHT-uSi20uvrPwfg6Fkk45F5o1LplJmhUeUTpKA2m4Bl/https%3A%2F%2Fmailman.drcmr.dk%2Fmailman%2Flistinfo%2Fsimnibs-discuss">
https://secure-web.cisco.com/1Mwi4oAKB2067fFkbaEJ3fhrzJKQDQrVgSXNK9STlqMnyBAi2L_meEk7y8CCdAj5u2hdEQKzxx03w9A1Zus9SDz97WSxDJz4W3cm55PeSt5_wFdxhnz7eOXeSKpX8e2pt_pdheNTMPh-LZP4s9RDbb7EDzljFPeg9v12LJ5z4sY9-zqMQ2dWPJVHtI3KzqJvgF9H_iw6N4vdnfZmLeISOoGZhBSbPAlA1gTOi84R-av18O0M3QEPqCRnLGWfJOAS3IpGPoiS2Sglu6B7dtOITlHT-uSi20uvrPwfg6Fkk45F5o1LplJmhUeUTpKA2m4Bl/https%3A%2F%2Fmailman.drcmr.dk%2Fmailman%2Flistinfo%2Fsimnibs-discuss</a><o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal">The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at <a href="https://www.massgeneralbrigham.org/complianceline">https://www.massgeneralbrigham.org/complianceline</a> .</p><br>
<p class="MsoNormal">Please note that this e-mail is not secure
(encrypted). If you do not wish to continue communication over
unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you
understand and accept this risk and wish to continue to communicate over
unencrypted e-mail. </p></body>
</html>