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<p>Dear Mana:<br>
</p>
<div class="moz-cite-prefix">On 1/22/2021 12:03 AM, Mana Biabani
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:5825440A-AFB6-47AB-819D-096494B68FF1@monash.edu">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi again!
<div class=""><br class="">
<div class="">I apologise for the additional email. I would like
to modify my question below regarding the coil position. </div>
<div class=""><br class="">
</div>
<div class="">Would appreciate if you could ignore my previous
email and help me with the points below:</div>
<div class=""><br class="">
</div>
<div class="">
<blockquote type="cite" class="">
<div class="" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break: after-white-space;">
<div class="">I am using SimNIBS to simulate TMS-induced
e-field and had two questions :</div>
<div class=""><br class="">
</div>
<div class="">1- Is there any method to measure the exact
distance between the coil and scalp surface? The 4mm
default distance is not appropriate for my experiment;
as the participants have EEG cap on and also there is a
foam between the coil and the cap. Also, I’d like to
account for the differences in the hair volume, etc. I
was thinking to measure the minimum euclidean distance
between the coil centre and the scalp coordinates but as
far as I understood the coil centre is actually a scalp
position. So, it shouldn’t work.</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
<p>When you have measured the distance physically during your
experiment or can estimate it otherwise, you can update the
distance used by SimNIBS by the proper value. See "distance" on
<a class="moz-txt-link-freetext" href="https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html">https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html</a><span
class="n"><br>
</span></p>
<p><span class="n">Example : </span>pos.distance = 10</p>
<p>--> 10 mm distance to skin</p>
<p>Note that you can also enter coordinates instead of electrode
positions for the centre and pos_ydir.<br>
</p>
<pre>
<span class="s1"></span></pre>
<blockquote type="cite"
cite="mid:5825440A-AFB6-47AB-819D-096494B68FF1@monash.edu">
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="" style="word-wrap: break-word;
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<div class=""><br class="">
</div>
<div class="">2- My second question was about the coil
orientation (in a more accurate way than choosing a
reference electrode …). I am using Brainsight to get the
information about the coil position, but not sure which
outputs represent coil angels around different axes. I
guess I can use [m0n0 m0n1 m0n2; m1n0 m1n1 m1n2; m2n0
m2n1 m2n2 ] from Brainsight to make the transformation
matrix, is that correct? If so, could you please let me
know how I should modify them to be compatible with the
coil axes in SimNIBS. <br>
</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
<p>When you have neuronavigation positions, you can directly set the
<strong>matsimnibs </strong>(also see
<a class="moz-txt-link-freetext" href="https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html">https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html</a><span
class="n">.)</span></p>
<p><span class="n"> Please also see </span><a class="moz-txt-link-freetext" href="https://simnibs.github.io/simnibs/build/html/_downloads/f0b89a9aa2f494cfe8e4dfd5d455e80e/coil_axesorientation.pdf">https://simnibs.github.io/simnibs/build/html/_downloads/f0b89a9aa2f494cfe8e4dfd5d455e80e/coil_axesorientation.pdf</a>
for a visualizatoin of the coil coordinate system used by SimNIBS.<br>
</p>
<p>I think that you can use Lox X, Loc Y & Loc Z and the m0n0
m0n1 m0n2, m1n0 ...... to directly set up the matsimnibs, but you
will likely have to exchange some of axes (i.e. m0 might not
correspond to px, but maybe -pz or so, depending on how the
convention in Brainsight is).<br>
</p>
<p>Hope this helps.<br>
</p>
<p>Best regards,</p>
<p>Axel<br>
</p>
<p><br>
</p>
<blockquote type="cite"
cite="mid:5825440A-AFB6-47AB-819D-096494B68FF1@monash.edu">
<div class="">
<div class="">
<blockquote type="cite" class="">
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<div class=""><br class="">
</div>
</div>
</blockquote>
<br class="">
</div>
<div class="">Kind regards,</div>
<div class="">Mana</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<br class="">
<br class="">
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class=""><span
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</span>
<div class=""
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<div class=""><b
class=""
style="font-size:
11px;">MANA
BIABANI</b></div>
<div class=""><span
class=""
style="font-size:
11px;">Research
Fellow</span></div>
<div class=""><span
class=""
style="font-size:
11px;"><br
class="">
</span></div>
<div class=""><strong
style="font-family: Calibri, sans-serif;" class=""><span
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Arial,
sans-serif;
font-size:
11px;"
class="">Turner
Institute for
Brain and
Mental Health</span></strong></div>
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University</span></div>
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class=""><span
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<div class=""
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class=""
style="font-size:
11px;">E: <a
href="mailto:mana.biabanimoghadam@monash.edu"
class=""
moz-do-not-send="true">mana.biabanimoghadam@monash.edu</a></span></div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On 21 Jan 2021, at 4:19 pm, Mana Biabani
<<a href="mailto:mana.biabanimoghadam@monash.edu"
class="" moz-do-not-send="true">mana.biabanimoghadam@monash.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; line-break: after-white-space;" class="">Hi, <br
class="">
<div class=""><br class="">
</div>
<div class="">I am using SimNIBS to simulate
TMS-induced e-field and had two questions :</div>
<div class=""><br class="">
</div>
<div class="">1- Is there any method to measure the
exact distance between the coil and scalp surface?
The 4mm default distance is not appropriate for my
experiment; as the participants have EEG cap on
and also there is a foam between the coil and the
cap. Also, I’d like to account for the differences
in the amount of hair, etc. I was thinking to
measure the minimum euclidean distance between the
coil centre and the scalp but as far as I
understood the coil centre coordinates are
actually scalp positions. So, it shouldn’t work.</div>
<div class=""><br class="">
</div>
<div class="">2- My second question was about coil
angle. I am using the angles that Brainsight
provides to make the transformation matrix as
below :</div>
<div class=""><br class="">
</div>
<div class="">[ m0n0<span class="Apple-tab-span" style="white-space: pre;"> </span>-m0n1<span class="Apple-tab-span" style="white-space: pre;"> </span>m0n2
<span class="Apple-tab-span" style="white-space:pre"> </span>coil.center(1)</div>
<div class=""> m1n0<span class="Apple-tab-span" style="white-space: pre;"> </span>-m1n1<span class="Apple-tab-span" style="white-space: pre;"> </span>m1n2<span class="Apple-tab-span" style="white-space:pre"> </span>coil.center(2)</div>
<div class=""> m2n0<span class="Apple-tab-span" style="white-space: pre;"> </span>-m2n1<span class="Apple-tab-span" style="white-space: pre;"> </span>m2n2<span class="Apple-tab-span" style="white-space:pre"> </span>coil.center(3)]
. </div>
<div class=""><br class="">
</div>
<div class="">Could you please confirm if this
matrix is correct. My understanding is that I
need to inverse the y axis in Brainsight and it
does not need any transformations (like MNI to
subject space). Is that correct?</div>
<div class=""><br class="">
</div>
<div class="">Greatly appreciate your help in
advance!</div>
<div class=""><br class="">
</div>
<div class="">Kind Regards,</div>
<div class="">Mana</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
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class=""><span
class=""
style="font-size:
11px;
font-family:
Helvetica;">---<br
class="">
</span>
<div class=""
style="font-size: 12px; font-family: Helvetica;">
<div class=""><b
class=""
style="font-size:
11px;">MANA
BIABANI</b></div>
<div class=""><span
class=""
style="font-size:
11px;">Research
Fellow</span></div>
<div class=""><span
class=""
style="font-size:
11px;"><br
class="">
</span></div>
<div class=""><strong
style="font-family: Calibri, sans-serif;" class=""><span
style="font-family:
Arial,
sans-serif;
font-size:
11px;"
class="">Turner
Institute for
Brain and
Mental Health</span></strong></div>
<div
style="margin:
0cm 0cm
0.0001pt;
line-height:
normal;
font-family:
Calibri,
sans-serif;"
class=""><span
style="font-family: Arial, sans-serif; font-size: 11px;" class="">Monash
University</span></div>
<div
style="margin:
0cm 0cm
0.0001pt;
line-height:
normal;
font-family:
Calibri,
sans-serif;"
class=""><span
style="font-family: Arial, sans-serif; font-size: 11px;" class="">18
Innovation
Walk</span></div>
<div
style="margin:
0cm 0cm
0.0001pt;
line-height:
normal;
font-family:
Calibri,
sans-serif;"
class=""><span
style="font-family: Arial, sans-serif; font-size: 11px;" class="">Clayton
VIC 3800</span></div>
<div
style="margin:
0cm 0cm
0.0001pt;
line-height:
normal;
font-family:
Calibri,
sans-serif;"
class=""><span
style="font-family: Arial, sans-serif; font-size: 11px;" class="">Australia</span></div>
<div
style="margin:
0cm 0cm
0.0001pt;
line-height:
normal;
font-family:
Calibri,
sans-serif;"
class=""><span
style="font-family: Arial, sans-serif; font-size: 11px;" class=""><br
class="">
</span></div>
</div>
<div class=""
style="font-size: 12px; font-family: Helvetica;"><span class=""
style="font-size:
11px;">E: <a
href="mailto:mana.biabanimoghadam@monash.edu"
class=""
moz-do-not-send="true">mana.biabanimoghadam@monash.edu</a></span></div>
<div class=""
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51);"><br
class="">
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51);"><br
class="">
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<pre class="moz-quote-pre" wrap="">_______________________________________________
Simnibs-discuss mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Simnibs-discuss@drcmr.dk">Simnibs-discuss@drcmr.dk</a>
<a class="moz-txt-link-freetext" href="https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss">https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr. Axel Thielscher
Associate Professor
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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