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<p>Dear Kris,</p>
<p>please see my comments below.</p>
<p>Best,</p>
<p>Axel<br>
</p>
<div class="moz-cite-prefix">On 1/13/2021 1:21 PM, Kris BAETENS
wrote:<br>
</div>
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<p class="MsoNormal">Dear SimNibs users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-GB">I want to compare
several tDCS montages and assess field strength in
particular ROI’s, on a “generic” head model, prior to
actually starting the study. I thought the MNI152 example
mesh could serve perfectly for this purpose. However, I
struggle with some very beginner technical issues.<o:p></o:p></span></p>
<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level1 lfo2"><span
lang="EN-GB">Am I correct in assuming that this mesh is
already in MNI space?
</span></li>
</ul>
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Yes.<br>
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<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level1 lfo2"><span
lang="EN-GB">“Transform to MNI space” under simulation
options fails, supposedly because the m2m folder doesn’t
contain the necessary information?</span></li>
</ul>
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As it is already in MNI space, there is no transformation required.
Just use "Interpolate to a nifti volume" instead.<br>
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<li class="MsoListParagraph"
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lfo2;text-autospace:none">
<span lang="EN-GB">Similarly, the mni2subject_coords call in
the example ROI script fails, again, I assume again
because the m2m folder doesn’t contain the necessary
information? (I can get it to run without a problem on
Ernie).</span></li>
</ul>
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</blockquote>
This call is not needed. Just use the coordinates without any
transformation.<br>
<blockquote type="cite"
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<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level1 lfo2"><span
lang="EN-GB">Is it possible to calculate mean field
strength in an anatomical (e.g., atlas-based) ROI, rather
than using the sphere-based approach? (I wanted to
approach this from a “masking” angle, but am unsure how to
proceed, as I cannot transform the standard head
simulation to MNI space).</span></li>
</ul>
</div>
</blockquote>
<p>Yes. The results which you get when using "Interpolate to a nifti
volume" are already in MNI space, and you can apply any ROI that
is in MNI space.<br>
</p>
<p>Best regards,</p>
<p>Axel<br>
</p>
<blockquote type="cite"
cite="mid:PA4PR01MB7840B5715B0DECA651C7A8CEF5A90@PA4PR01MB7840.eurprd01.prod.exchangelabs.com">
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<p class="MsoListParagraph"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Thank you very much for
making this wonderful software and also making the tutorials
publicly available on youtube!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Kris Baetens<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
Simnibs-discuss mailing list
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<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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