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<p>Hi Ines,</p>
<p>when you open the nifti-file in freeview, is it then coregistered
with the <subid>_T1fs_conform.nii.gz which headreco creates?
If not, you can first run freesurfer and use the T1 and T2 which
freesurfer stores as input to headreco.</p>
<p>You can then try the nii2msh tool, which puts the data from
niftis into the mesh. <br>
</p>
<p>Let us know in case you get stuck.<br>
</p>
<p>Best regards,</p>
<p>Axel</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 12/9/2020 6:40 PM, Inês Violante
wrote:<br>
</div>
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">Hello,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">I’ve just
tried headreco and it is really cool.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">I would like
to have a segmentation of the hippocampus in the same space
as the meshes generated by headreco.
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">I have the
hippocampus segmentation from freesurfer aligned to the
subject space. This is a .nii.gz file
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">How can I now
convert this to stl and have it in the same space as the
other meshes generated by headreco?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">Thank you in
advance!<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">All the best,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">ines<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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<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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