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<p>Dear Jade,</p>
<p><br>
</p>
<p>Thanks a lot for your interest in SimNIBS.</p>
<p><br>
</p>
<p><i>in the position window, and next to the dropdown box for the
EEG cap positions, are these x y z coordinates that I can input
in MNI space?</i><br>
</p>
<p><br>
</p>
<p>These positions are in world space of the input scan. However,
you can easily transform between subject space and MNI space.
Please see here for more information:</p>
<p><a class="moz-txt-link-freetext" href="https://simnibs.github.io/simnibs/build/html/documentation/coordinates.html">https://simnibs.github.io/simnibs/build/html/documentation/coordinates.html</a></p>
<p><br>
</p>
<p>You could also skip the GUI completely and setup simulations with
python or matlab scripts where you input MNI coordinates directly.
Examples:<br>
</p>
<p><br>
</p>
<p><a class="moz-txt-link-freetext" href="https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TMS_MNI.m">https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TMS_MNI.m</a></p>
<p><a class="moz-txt-link-freetext" href="https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TMS_MNI.py">https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TMS_MNI.py</a></p>
<p><br>
</p>
<p><br>
</p>
<p><span style="color: rgb(0, 0, 0);"><i>Also, if I generate a model
with stimulation to specific coordinates and then calculate
the norm Efield at the control ROI, what does the output
equate to? How can I know if this is equivalent to say their
motor threshold? <br>
</i></span></p>
<p><span style="color: rgb(0, 0, 0);"><i><br>
</i></span></p>
<p><span style="color: rgb(0, 0, 0);">The output is an electric
field in V/m. We know that electric fields and motor threshold
in TMS are correlated (see </span><br>
<span style="color: rgb(0, 0, 0);"> <a
href="https://doi.org/10.1093/cercor/bhw292">https://doi.org/10.1093/cercor/bhw292</a>,
</span><span style="color: rgb(0, 0, 0);"><a class="doi"
href="https://doi.org/10.1016/j.neuroimage.2019.116486"
target="_blank" rel="noreferrer noopener"
aria-label="Persistent link using digital object identifier"
title="Persistent link using digital object identifier">https://doi.org/10.1016/j.neuroimage.2019.116486</a>,
</span><span style="color: rgb(0, 0, 0);"><a class="doi"
href="https://doi.org/10.1016/j.neuroimage.2019.116486"
target="_blank" rel="noreferrer noopener"
aria-label="Persistent link using digital object identifier"
title="Persistent link using digital object identifier">https://doi.org/</a></span><span
style="color: rgb(0, 0, 0);"><a
href="https://doi.org/10.1016/j.brs.2017.09.011"
target="_blank" rel="noreferrer noopener">10.1016/j.brs.2017.09.011</a>).
But the relationship between the two is complex. So we can't say
at the moment that if the electric field in a given region (for
example hand knob) is above a certain value you will for sure an
MEP, but rather that a larger electric field increases the
probability of getting an MEP.<br>
</span></p>
<p><span style="color: rgb(0, 0, 0);"><br>
</span></p>
<p><span style="color: rgb(0, 0, 0);">Best Regards,</span></p>
<p><span style="color: rgb(0, 0, 0);">Guilherme</span></p>
<p><span style="color: rgb(0, 0, 0);"><br>
</span></p>
<p><span style="color: rgb(0, 0, 0);"><br>
</span></p>
<div class="moz-cite-prefix">On 03/03/2020 16.05, Jade Jackson
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:4911e81ba4514a528f13648cf5ca45cb@mrc-cbu.cam.ac.uk">
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<p><span style="caret-color: rgb(255, 255, 255); color: rgb(0,
0, 0); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">Dear developers, </span></p>
<div style="caret-color: rgb(255, 255, 255); color: rgb(255,
255, 255); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">
<br>
</div>
<div style="caret-color: rgb(255, 255, 255); color: rgb(255,
255, 255); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">
<span style="color: rgb(0, 0, 0);">Thank you for developing
this toolbox. I have specific MNI coordinates that I want to
stimulate and I want to understand whether the stimulation
will spread to a control ROI, and if so, to what degree. </span></div>
<div style="caret-color: rgb(255, 255, 255); color: rgb(255,
255, 255); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">
<br>
</div>
<div style="caret-color: rgb(255, 255, 255); color: rgb(255,
255, 255); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">
<span style="color: rgb(0, 0, 0);">I have a couple of very
basic questions, in the position window, and next to the
dropdown box for the EEG cap positions, are these x y z
coordinates that I can input in MNI space? Also, if I
generate a model with stimulation to specific coordinates
and then calculate the norm Efield at the control ROI, what
does the output equate to? How can I know if this is
equivalent to say their motor threshold? </span></div>
<div style="caret-color: rgb(255, 255, 255); color: rgb(255,
255, 255); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">
<br>
</div>
<div style="caret-color: rgb(255, 255, 255); color: rgb(255,
255, 255); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">
<span style="color: rgb(0, 0, 0);">Thanks, </span></div>
<div style="caret-color: rgb(255, 255, 255); color: rgb(255,
255, 255); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">
<br>
</div>
<div style="caret-color: rgb(255, 255, 255); color: rgb(255,
255, 255); font-family: Helvetica; font-size: 12px;
text-size-adjust: auto;">
<span style="color: rgb(0, 0, 0);">Jade</span></div>
<br>
</div>
<br>
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