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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>
    <blockquote type="cite"
cite="mid:LOYP123MB34074B0EEC2FDB18E10734BDAFCC0@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM">
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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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      <pre class="moz-quote-pre" wrap="">_______________________________________________
Simnibs-discuss mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Simnibs-discuss@drcmr.dk">Simnibs-discuss@drcmr.dk</a>
<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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