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<p>Dear Valerie,</p>
<p>thanks for contacting us. It seems that we might have to update
meshfix to work with Catalina. We'll come back to you. In the
meantime, could you quickly check whether <span class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">subcortical_FS.stl
looks "normal" (i.e. is a closed surface) when you open it in
gmsh? (gmsh is also part of simnibs). Otherwise, please let us
know.<br>
</span></p>
<p>Best,</p>
<p>Axel</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 5/7/2020 6:48 PM, Valerie Nicolson
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CA+We4dV5=G2oiON7g-OsEM6c8TxPcywu4ce+b3eJ9yp773F-0Q@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hello,
<div><br>
</div>
<div>I am a new simnibs user on a Mac running Catalina 10.15.4.
After installation (and verifying the simnibs gui using ernie)
I tried creating a mesh using mri2mesh using ernie's T1 only </div>
<div><br>
</div>
<div>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">mri2mesh
--all ernie org/ernie_T1.nii.g</span></p>
</div>
<div><br>
</div>
<div>After many hours and lots of output it crashes. This is the
last of the output:</div>
<div><br>
</div>
<div>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">meshfix
subcortical_FS.stl</span></p>
<p class="gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">ERROR-
fseek
/Users/guilherme/simnibs_supporting/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335
failed.exiting mri2mesh after error</span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><br>
</span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><br>
</span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">I
checked, and subcortical_FS.stl exists and is definitely
longer than 80 (this seems to be the fseek call in io.cpp
that is failing). I've also tried running meshfix on other
.stl files and get the same error, so I'm getting the idea
that meshfix is trying to open some other file). Any ideas
of how to fix this or what file might be missing from my
installation?</span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><br>
</span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Thanks,</span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><br>
</span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">Valerie
Cardenas Nicolson</span></p>
</div>
</div>
<br>
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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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