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<p>Dear Ines,</p>
<p>the description in the simnibs documentation is not very clear, I
am sorry for this. You can use nii2mesh -h to get a bit more
information (not not much though). Please try calling it without
the -ev.<br>
</p>
<p>Best regards,</p>
<p>Axel<br>
</p>
<div class="moz-cite-prefix">On 12/14/2020 12:51 PM, Inês Violante
wrote:<br>
</div>
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<div class="WordSection1">
<p class="MsoNormal"><span style="font-family:Helvetica">Hi
Axel,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">Thanks
for the quick reply.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">I tried
that but with no luck. See command line output below.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">nii2msh -ev
TIDES_P2T_S1_FreeSf/TIDES_P2T_S1/mri/lHippocampus.nii.gz
TIDES_P2T_S1.msh lHipp.msh<o:p></o:p></span></p>
<p class="p1"><span class="s1"><o:p> </o:p></span></p>
<p class="p1"><span class="s1">[ simnibs ]INFO: Creating tensor
visualization</span></p>
<p class="p1"><span class="s1">Traceback (most recent call
last):</span></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">File
"/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py",
line 92, in <module></span></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">main()</span></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">File
"/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py",
line 71, in main</span></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">aniso_tissues=[1, 2])</span></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">File
"/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/simulation/cond.py",
line 173, in cond2elmdata</span></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">assert len(anisotropy_volume.shape) == 4</span></p>
<p class="p1"><span class="s1">AssertionError</span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">Could
this be because the volume is smaller than the expected from
the T1 mesh?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">All the
best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">Ines<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica;color:black;mso-fareast-language:EN-GB">--<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica;color:black;mso-fareast-language:EN-GB">Dr
Ines Violante<br>
Lecturer in Psychological Neuroscience <br>
School of Psychology | Faculty of Health and Medical
Sciences<br>
Room 32 AC 04<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica;color:black;mso-fareast-language:EN-GB">University
of Surrey | Guildford GU2 7XH<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span
style="color:black">From:
</span></b><span style="color:black">Axel Thielscher
<a class="moz-txt-link-rfc2396E" href="mailto:axelt@drcmr.dk"><axelt@drcmr.dk></a><br>
<b>Date: </b>Friday, 11 December 2020 at 20:39<br>
<b>To: </b><a class="moz-txt-link-abbreviated" href="mailto:simnibs-discuss@drcmr.dk">simnibs-discuss@drcmr.dk</a>
<a class="moz-txt-link-rfc2396E" href="mailto:simnibs-discuss@drcmr.dk"><simnibs-discuss@drcmr.dk></a>, <a class="moz-txt-link-abbreviated" href="mailto:inesviolante@gmail.com">inesviolante@gmail.com</a>
<a class="moz-txt-link-rfc2396E" href="mailto:inesviolante@gmail.com"><inesviolante@gmail.com></a><br>
<b>Subject: </b>Re: [Simnibs-discuss] hippocampal
segmentation to stl</span><span
style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
</div>
<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.
</p>
<p>Let us know in case you get stuck.</p>
<p>Best regards,</p>
<p>Axel</p>
<p><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 12/9/2020 6:40 PM, Inês Violante
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">Hello,</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"> </span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">I’ve just
tried headreco and it is really cool.</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.
</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
</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"> </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?</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"> </span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">Thank you
in advance!</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"> </span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">All the
best,</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica"> </span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:Helvetica">ines</span></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span
style="font-size:11.0pt;mso-fareast-language:EN-GB"><br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________</pre>
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</blockquote>
<pre>-- </pre>
<pre>Dr. Axel Thielscher</pre>
<pre>Associate Professor</pre>
<pre>Danish Research Center for Magnetic Resonance</pre>
<pre>Copenhagen University Hospital Hvidovre</pre>
<pre>DK-2650 Hvidovre, Denmark</pre>
<pre><a href="http://www.drcmr.dk" moz-do-not-send="true">www.drcmr.dk</a></pre>
<pre>&</pre>
<pre>Department of Health Technology</pre>
<pre>Technical University of Denmark</pre>
<pre>DK-2800 Kgs. Lyngby</pre>
<pre><a href="http://www.healthtech.dtu.dk/" moz-do-not-send="true">http://www.healthtech.dtu.dk/</a></pre>
<p class="MsoNormal"><span
style="font-size:11.0pt;mso-fareast-language:EN-GB">--><o:p></o:p></span></p>
</div>
</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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