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<p>Hi,</p>
<p>you could adjust the dI/dt when setting up the simulations to
realistic values (the standard in the GUI is 1 A/mue_s, which is
very low; values exceeding ~70 A/Mue_s would be realistic for
standard coils). You will then also have to adjust the threshold
in the script to a more realistic value for a e-field strength
that would result in neural excitation. You can try ~60 V/m, for
example. However, as long as the dI/dt of both simulations is the
same, the outcome will be identical to that of the original script
when selecting the threshold accordingly (as setting the dI/dt
only linearly scales the simulated fields) - the selected
threshold is somewhat arbitrary as the exact cortical excitation
thresholds are not fully known and just determines how large the
overlap region is.<br>
</p>
<p>When you don't use the same stimulation intensity for both
stimulations, then it would be for sure important to set the dI/dt
values, as this will then also shift the position of the overlap
region.</p>
<p>Best regards,</p>
<p>Axel<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 6/10/2021 11:58 AM, Dantas, A (MW)
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:700968ed497541309526b52395e0a60e@UM-MAIL3217.unimaas.nl">
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<div class="WordSection1">
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Dear Axel,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">One more question: What about the stimulation
intensities? Can we adjust the intensity to check if the
overlap is influenced by it?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="en-NL"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><b><span
style="font-size:10.0pt;color:#F47321" lang="EN">Aline
Dantas </span></b><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span
style="font-size:10.0pt;color:#939598" lang="EN">PhD
candidate</span></i><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span
style="font-size:10.0pt;color:#939598" lang="EN">Human
Decision and Policy Design</span></i><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span
style="font-size:10.0pt;color:#939598" lang="EN">Departments
of Marketing and Supply Chain Management (SBE) and
Cognitive Neurosciences (FPN)</span></i><span
lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;color:#939598" lang="EN">Room
F2.02. Tongersestraat 53, 6211 LM </span><span
lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;color:#939598" lang="EN">Room
2.018. Oxfordlaan 55, 6229 EV </span><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="en-NL"> <o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="en-NL"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span
lang="EN-US"> Dantas, A (MW)
<br>
<b>Sent:</b> Wednesday, 2 June 2021 15:10<br>
<b>To:</b> 'Axel Thielscher' <a class="moz-txt-link-rfc2396E" href="mailto:axelt@drcmr.dk"><axelt@drcmr.dk></a>;
<a class="moz-txt-link-abbreviated" href="mailto:discuss@simnibs.org">discuss@simnibs.org</a>; <a class="moz-txt-link-abbreviated" href="mailto:jonas.persson@neuro.uu.se">jonas.persson@neuro.uu.se</a><br>
<b>Cc:</b> Ébner, Nancy (Stud. FHML / Alumni UCV)
<a class="moz-txt-link-rfc2396E" href="mailto:n.ebner@student.maastrichtuniversity.nl"><n.ebner@student.maastrichtuniversity.nl></a><br>
<b>Subject:</b> RE: [Simnibs-discuss] SimNIBS simulation
- TMS study - Overlap figure<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Thank you very much! I’ll try this solution.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Aline Dantas<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="en-NL"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span
lang="EN-US"> Axel Thielscher <<a
href="mailto:axelt@drcmr.dk" moz-do-not-send="true">axelt@drcmr.dk</a>>
<br>
<b>Sent:</b> Wednesday, 2 June 2021 14:50<br>
<b>To:</b> Dantas, A (MW) <<a
href="mailto:a.dantas@maastrichtuniversity.nl"
moz-do-not-send="true">a.dantas@maastrichtuniversity.nl</a>>;
<a href="mailto:discuss@simnibs.org"
moz-do-not-send="true">discuss@simnibs.org</a>; <a
href="mailto:jonas.persson@neuro.uu.se"
moz-do-not-send="true">
jonas.persson@neuro.uu.se</a><br>
<b>Cc:</b> Ébner, Nancy (Stud. FHML / Alumni UCV) <<a
href="mailto:n.ebner@student.maastrichtuniversity.nl"
moz-do-not-send="true">n.ebner@student.maastrichtuniversity.nl</a>><br>
<b>Subject:</b> Re: [Simnibs-discuss] SimNIBS simulation
- TMS study - Overlap figure<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
<p><span lang="en-NL">Hi,<o:p></o:p></span></p>
<p><span lang="en-NL">for determining an overlap, you will have
to set a threshold to then show the regions where both TMS
fields exceed this threshold. In the attached example code
, I've used 0.75 as threshold, please adjust this according
to your needs.
<o:p></o:p></span></p>
<p><span lang="en-NL">Regions where the first stimulation
exceeds the threshold are coded as 1, regions where the
second stimulation exceeds the threshold are coded as 2, the
overlap is coded as 3.<o:p></o:p></span></p>
<p><span lang="en-NL"><img
style="width:5.8177in;height:3.6354in"
id="Picture_x0020_1"
src="cid:part6.CA6A6DE7.62593491@drcmr.dk" class=""
width="559" height="349" border="0"></span><span
lang="en-NL"><o:p></o:p></span></p>
<p><span lang="en-NL">Best regards,<o:p></o:p></span></p>
<p><span lang="en-NL">Axel<o:p></o:p></span></p>
<p><span lang="en-NL"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span lang="en-NL">On 5/26/2021 2:33 PM,
Dantas, A (MW) wrote:<o:p></o:p></span></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Dear all,
</span><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">My student Nancy Ébner got in touch with you
recently about the need for a Magventure double cone coil
simulation using SimNIBS.
</span><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">We ran the simulations successfully, so first
of all I would like to thank you!</span><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">We have an experiment deactivating the VMPFC
vs. deactivating the right DLPFC. So far, we managed to
run both simulations, but it would be great if we could
the overlap image of stimulating these two areas. We tried
to make it but did not succeed. </span><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Do you think you could help me to build that?</span><span
lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US"> </span><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Thank you!</span><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Kind regards,</span><span lang="en-NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"
lang="EN-US">Aline Dantas</span><span lang="en-NL"><o:p></o:p></span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"
lang="en-NL"> </span><span lang="en-NL"><o:p></o:p></span></p>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span
lang="en-NL"><o:p> </o:p></span></p>
<pre><span lang="en-NL">_______________________________________________<o:p></o:p></span></pre>
<pre><span lang="en-NL">Simnibs-discuss mailing list<o:p></o:p></span></pre>
<pre><span lang="en-NL"><a href="mailto:Simnibs-discuss@drcmr.dk" moz-do-not-send="true">Simnibs-discuss@drcmr.dk</a><o:p></o:p></span></pre>
<pre><span lang="en-NL"><a href="https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss" moz-do-not-send="true">https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss</a><o:p></o:p></span></pre>
</blockquote>
<pre><span lang="en-NL">-- <o:p></o:p></span></pre>
<pre><span lang="en-NL">Dr. Axel Thielscher<o:p></o:p></span></pre>
<pre><span lang="en-NL">Professor of Neurophysics and Neuroimaging<o:p></o:p></span></pre>
<pre><span lang="en-NL">Danish Research Center for Magnetic Resonance<o:p></o:p></span></pre>
<pre><span lang="en-NL">Copenhagen University Hospital Hvidovre<o:p></o:p></span></pre>
<pre><span lang="en-NL">DK-2650 Hvidovre, Denmark<o:p></o:p></span></pre>
<pre><span lang="en-NL"><a href="http://www.drcmr.dk" moz-do-not-send="true">www.drcmr.dk</a><o:p></o:p></span></pre>
<pre><span lang="en-NL">&<o:p></o:p></span></pre>
<pre><span lang="en-NL">Department of Health Technology<o:p></o:p></span></pre>
<pre><span lang="en-NL">Technical University of Denmark<o:p></o:p></span></pre>
<pre><span lang="en-NL">DK-2800 Kgs. Lyngby<o:p></o:p></span></pre>
<pre><span lang="en-NL"><a href="http://www.healthtech.dtu.dk/" moz-do-not-send="true">http://www.healthtech.dtu.dk/</a><o:p></o:p></span></pre>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
<a class="moz-txt-link-abbreviated" href="http://www.drcmr.dk">www.drcmr.dk</a>
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
<a class="moz-txt-link-freetext" href="http://www.healthtech.dtu.dk/">http://www.healthtech.dtu.dk/</a></pre>
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