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<p class="MsoNormal"><span style="font-size:11.0pt">I’ve attached the terminal output here in case it helps uncover what’s happening here.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Mags<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Simnibs-discuss <simnibs-discuss-bounces@drcmr.dk> on behalf of Mags McAllister <margaret.mcallister@duke.edu><br>
<b>Date: </b>Thursday, February 9, 2023 at 3:54 PM<br>
<b>To: </b>discuss@simnibs.org <discuss@simnibs.org><br>
<b>Subject: </b>[Simnibs-discuss] Charm Issue<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hello, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I have come across a very strange issue creating the reconstruction with charm. I input a T1 with full coverage of the skull, but the model it created looks like this. The T1_upsampled, T1_bias_corrected,
and T1 nifti files in the m2m folder all show the full scan. The surface files however reflect only the bottom half of the brain like what I view in the simnibs gui.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I’m re-running this now with the same issue and can share the terminal output when it concludes. The command I used was ‘charm subID T1.nii.gz’.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I appreciate any advice or thoughts others have!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Mags M. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><img width="544" height="347" style="width:5.6666in;height:3.6145in" id="Picture_x0020_1" src="cid:image001.png@01D93C9C.F405DD10" alt="A picture containing colorful
Description automatically generated"><o:p></o:p></span></p>
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