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<p>Which SimNIBS version are you using? In 3.1 we switched to using
linear interpolation, so these artifacts should not happen
anymore.</p>
<p><br>
</p>
<p>Best Regards,</p>
<p>Guilherme<br>
</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 19/03/2020 10.31, Jane Tan wrote:<br>
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font-size: 12pt; color: rgb(0, 0, 0);">
Hi Guilherme,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Thanks for the reply. There are a good number of negative values
(~22.5%).</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial,
Helvetica, sans-serif; font-size: 12pt;">Do you have any
suggestions on what I can do to attenuate the artifacts? My
main aim is to get the mean e-field for specific ROIs.</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial,
Helvetica, sans-serif; font-size: 12pt;">For instance, would
you recommend the use of normJ instead? I notice that there
are fewer negative values for normJ, and notably none in the
ROIs I am interested in. </span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial,
Helvetica, sans-serif; font-size: 12pt;"><br>
</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial,
Helvetica, sans-serif; font-size: 12pt;">best regards,</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial,
Helvetica, sans-serif; font-size: 12pt;">Jane</span></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
Guilherme B Saturnino <a class="moz-txt-link-rfc2396E" href="mailto:guilhermebs@drcmr.dk"><guilhermebs@drcmr.dk></a><br>
<b>Sent:</b> Thursday, 19 March 2020 4:08 PM<br>
<b>To:</b> Jane Tan <a class="moz-txt-link-rfc2396E" href="mailto:Jane.Tan@murdoch.edu.au"><Jane.Tan@murdoch.edu.au></a>;
<a class="moz-txt-link-abbreviated" href="mailto:discuss@simnibs.org">discuss@simnibs.org</a> <a class="moz-txt-link-rfc2396E" href="mailto:discuss@simnibs.org"><discuss@simnibs.org></a><br>
<b>Subject:</b> Re: [Simnibs-discuss] normE values in MNI
space</font>
<div> </div>
</div>
<div>
<p>Dear Jane,</p>
<p><br>
</p>
<p><br>
</p>
<p>How many negative values are there? This is likely an
artifact due to spline interpolation of the electric field
from the original space to MNI space.</p>
<p><br>
</p>
<p>Best Regards,</p>
<p>Guilherme</p>
<p><br>
</p>
<div class="x_moz-cite-prefix">On 19/03/2020 06.06, Jane Tan
wrote:<br>
</div>
<blockquote type="cite">
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Hi SimNIBS Team,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
I found some negative values in my <span
style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important">nifti volume for normE in MNI
space, and I thought something must have gone awry during
the segmentation process for my head mesh (created <span
style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important">using headreco (with cat) on a
MNI152 T1-weighted image)</span>. However, the head
mesh looks okay when I checked it with gmsh. The
headreco_log doesn't seem to indicate any issues either -
at least not to my untrained eye. I do not have access to
freeview, and couldn't do a proper check via headreco.</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important">I'm also wondering if it might
be due to normE not being very accurate as a result of
registration to the MNI template? </span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important">Your suggestions would be
greatly appreciated. I am happy to provide my head mesh
and segmentation results if that would be of any help.</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important">best regards,</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Jane</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
background-color:rgb(255,255,255);
display:inline!important"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
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<p class="x_MsoNormal" style="margin-top:0px;
margin-bottom:0px"><span style="" lang="EN-SG">Best
regards,</span></p>
<p class="x_MsoNormal" style="margin-top:0px;
margin-bottom:0px"><span style="" lang="EN-SG"><br>
</span></p>
<p class="x_MsoNormal" style="margin-top:0px;
margin-bottom:0px"><span style="" lang="EN-SG">Jane</span></p>
<p class="x_MsoNormal" style="margin-top:0px;
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<b><b style="color:rgb(33,33,33);
font-family:Calibri,sans-serif,serif,EmojiFont;
font-size:14.6667px"><span
style="font-size:10pt"><span
style="color:rgb(51,51,51)"><br>
</span></span></b></b></p>
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