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<div class="moz-cite-prefix">Dear Richard,<br>
<br>
when I remember right, without having now deeply checked, cstoss
is one of the SimBio-Fortran rountines that is<br>
responsible for the compressed storage of symmetric stiffness
matrices (efficient storage when a matrix has only <br>
few non-zero elements per row, and in FEM it is like that). If it
contains an "empty row", then something went wrong<br>
with building the stiffness matrix. Might you have elements with
zero-conductivity, for example a sinus hole?<br>
Then the simplest solution is that you give those elements low ,
e.g. 10^-8, conductivity or similar.<br>
<br>
Some advertisement for the new: I have to admit it is a longer
time ago that I stepped through the SimBio code, especially
because we are working <br>
towards a replacement of the SimBio-FEM with DUNEuro
<a class="moz-txt-link-freetext" href="http://www.duneuro.org/">http://www.duneuro.org/</a>, which is a more up-to-date <br>
C++ code for FEM forward modeling and offers more different FEM
options than SimBio-NeuroFEM, where the latter<br>
only continuous Galerkin-FEM). We currently have a software
publication for DUNEuro in revision, if accepted,<br>
I could send to you.<br>
<br>
<br>
BR<br>
Carsten<br>
<br>
Am 31.03.21 um 18:41 schrieb RICHARDS, JOHN:<br>
</div>
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<p class="MsoNormal">I am trying to create a segmented head
volume with tetra mesh.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">1—about 2-3 mo ago, I had been doing this
seamlessly. The ft_prepare_mesh used the
prepare_mesh_tetrahedral consistent with the ft 20210330
version.<o:p></o:p></p>
<p class="MsoNormal">Then ran the ft_prepare_headmodel with the
resulting mesh.<o:p></o:p></p>
<p class="MsoNormal">It worked, produced a volume<o:p></o:p></p>
<p class="MsoNormal">cfg = [];<o:p></o:p></p>
<p class="MsoNormal">cfg.method ='simbio';<o:p></o:p></p>
<p class="MsoNormal">cfg.conductivity=conductivity1;<o:p></o:p></p>
<p class="MsoNormal">try<o:p></o:p></p>
<p class="MsoNormal">vol = ft_prepare_headmodel(cfg,
mesh); <o:p></o:p></p>
<p class="MsoNormal">catch ME <o:p></o:p></p>
<p class="MsoNormal">rethrow(ME)<o:p></o:p></p>
<p class="MsoNormal">return;<o:p></o:p></p>
<p class="MsoNormal">end <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">2—I am trying the same thing now, with the
same MRIs and segmenting, and etc.
<o:p></o:p></p>
<p class="MsoNormal">The GUI matlab is running.<o:p></o:p></p>
<p class="MsoNormal">STOP Leere Zeile in cstoss is printed in
the xterm command line window<o:p></o:p></p>
<p class="MsoNormal">The matlab program stops, gives errors like
below.<o:p></o:p></p>
<p class="MsoNormal">Suggesting it is occurring in the mex file
for the simbio mex file.?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">3—I have tried a dozen different
combinations of the mesh call to the iso2mesh,<o:p></o:p></p>
<p class="MsoNormal">[node, elem, face] = vol2mesh(seg,
1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3), 2, 2, isovalue);<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">isovalues = 0.5;<o:p></o:p></p>
<p class="MsoNormal">maxvol=64;<o:p></o:p></p>
<p class="MsoNormal">dofix=1;<o:p></o:p></p>
<p class="MsoNormal">opt=100;<o:p></o:p></p>
<p class="MsoNormal">method='cgalmesh';<o:p></o:p></p>
<p class="MsoNormal">ix=[1:mri.dim(1)];<o:p></o:p></p>
<p class="MsoNormal">iy=[1:mri.dim(2)];<o:p></o:p></p>
<p class="MsoNormal">iz=[1:mri.dim(3)];<o:p></o:p></p>
<p class="MsoNormal">img=uint8(seg);<o:p></o:p></p>
<p class="MsoNormal">[node,elem,face]=vol2mesh(img,ix,iy,iz,opt,maxvol,dofix,method,isovalues);<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">[node, elem, face] = vol2mesh(uint8(seg),
1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3), 1, 1, 0,
'cgalmesh');<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">[node, elem, face] = vol2mesh(uint8(seg),
1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3),
isovalues,opt,maxvol, 'cgalmesh');<o:p></o:p></p>
<p class="MsoNormal">[node,elem,face]=v2m(uint8(seg),0.5,100,128,method);<o:p></o:p></p>
<p class="MsoNormal">[node, elem, face] = vol2mesh(uint8(seg),
1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3), 1, 1, 0,
'cgalmesh');<o:p></o:p></p>
<p class="MsoNormal">[node, elem, face] = vol2mesh(uint8(seg),
1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3), 2, 2, 0,'cgalmesh');<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">4—I may have changed the matlab version
since the ones that worked. However, this does not explain
that a former mesh works in the current prepare_headmodel,
whereas a current mesh does not.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any ideas?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">John<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Matlab crash dump<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">--------------------------------------------------------------------------------<o:p></o:p></p>
<p class="MsoNormal"> Segmentation violation detected at
Wed Mar 31 12:30:03 2021 -0400<o:p></o:p></p>
<p class="MsoNormal">--------------------------------------------------------------------------------<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Configuration:<o:p></o:p></p>
<p class="MsoNormal"> Crash Decoding : Disabled - No
sandbox or build area path<o:p></o:p></p>
<p class="MsoNormal"> Crash Mode : continue
(default)<o:p></o:p></p>
<p class="MsoNormal"> Default Encoding : UTF-8<o:p></o:p></p>
<p class="MsoNormal"> Deployed : false<o:p></o:p></p>
<p class="MsoNormal"> GNU C Library : 2.17 stable<o:p></o:p></p>
<p class="MsoNormal"> Graphics Driver : Unknown
software <o:p></o:p></p>
<p class="MsoNormal"> Graphics card 1 : 0x102b (
0x102b ) 0x533 Version 0.0.0.0 (0-0-0)<o:p></o:p></p>
<p class="MsoNormal"> Java Version : Java
1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit
Server VM mixed mode<o:p></o:p></p>
<p class="MsoNormal"> MATLAB Architecture : glnxa64<o:p></o:p></p>
<p class="MsoNormal"> MATLAB Entitlement ID : 4290990<o:p></o:p></p>
<p class="MsoNormal"> MATLAB Root :
/share/apps/MATLAB/R2019b<o:p></o:p></p>
<p class="MsoNormal"> MATLAB Version : 9.7.0.1190202
(R2019b)<o:p></o:p></p>
<p class="MsoNormal"> OpenGL : software<o:p></o:p></p>
<p class="MsoNormal"> Operating System : "CentOS Linux
release 7.3.1611 (Core) "<o:p></o:p></p>
<p class="MsoNormal"> Process ID : 14136<o:p></o:p></p>
<p class="MsoNormal"> Processor ID : x86 Family 6
Model 79 Stepping 1, GenuineIntel<o:p></o:p></p>
<p class="MsoNormal"> Session Key :
06410f0f-59e8-40e7-b19f-3bbab586464d<o:p></o:p></p>
<p class="MsoNormal"> Static TLS mitigation : Enabled: Full<o:p></o:p></p>
<p class="MsoNormal"> Window System : Moba/X
(11603000), display localhost:15.0<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Fault Count: 1<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Abnormal termination:<o:p></o:p></p>
<p class="MsoNormal">Segmentation violation<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Register State (from fault):<o:p></o:p></p>
<p class="MsoNormal"> RAX = 00002aaad18c1650 RBX =
00002aaad24e5190<o:p></o:p></p>
<p class="MsoNormal"> RCX = 00002aaad8db7558 RDX =
0000000000000020<o:p></o:p></p>
<p class="MsoNormal"> RSP = 00002aaad8db1f38 RBP =
00002aaad8db1fa0<o:p></o:p></p>
<p class="MsoNormal"> RSI = 0000000000000025 RDI =
00002aaad1941530<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> R8 = 00002aaac005e060 R9 =
00002aaad000daa0<o:p></o:p></p>
<p class="MsoNormal"> R10 = 00002aaad8db1d40 R11 =
00002aaaadd45e50<o:p></o:p></p>
<p class="MsoNormal"> R12 = 00002aaad193ac80 R13 =
0000000000000000<o:p></o:p></p>
<p class="MsoNormal"> R14 = 0000000000000000 R15 =
000000000000623e<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> RIP = 00002aaad1997570 EFL =
0000000000010202<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> CS = 0033 FS = 0000 GS = 0000<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Stack Trace (from fault):<o:p></o:p></p>
<p class="MsoNormal">[ 0]
0x00002aaad1997570
<unknown-module>+00000000<o:p></o:p></p>
<p class="MsoNormal">[ 1] 0x00002aaaabbfd5ee
/share/apps/MATLAB/R2019b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+01095150
_ZNSo5flushEv+00000030<o:p></o:p></p>
<p class="MsoNormal">[ 2]
0x0000000000000000
<unknown-module>+00000000<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This error was detected while a MEX-file
was running. If the MEX-file<o:p></o:p></p>
<p class="MsoNormal">is not an official MathWorks function,
please examine its source code<o:p></o:p></p>
<p class="MsoNormal">for errors. Please consult the External
Interfaces Guide for information<o:p></o:p></p>
<p class="MsoNormal">on debugging MEX-files.<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span
style="font-size:10.0pt;font-family:Consolas;color:black">***********************************************<br>
John E. Richards<br>
Carolina Distinguished Professor<br>
Department of Psychology<br>
University of South Carolina<br>
Columbia, SC 29208<br>
Dept Phone: 803 777 2079<br>
Fax: 803 777 9558<br>
Email: </span><a href="mailto:richards-john@sc.edu"
moz-do-not-send="true"><span
style="font-size:10.0pt;font-family:Consolas;color:#0563C1">richards-john@sc.edu</span></a><u><span
style="font-size:10.0pt;font-family:Consolas;color:blue"><br>
</span></u><span
style="font-size:10.0pt;font-family:Consolas;color:black"><a
href="https://jerlab.sc.edu" moz-do-not-send="true"><span
style="color:#0563C1">https://jerlab.sc.edu</span></a><br>
*************************************************</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
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<br>
<br>
<pre class="moz-signature" cols="72">--
Prof. Dr.rer.nat. Carsten H. Wolters
University of Münster
Institute for Biomagnetism and Biosignalanalysis
Malmedyweg 15
48149 Münster, Germany
Phone:
+49 (0)251 83 56904
+49 (0)251 83 56865 (secr.)
Fax:
+49 (0)251 83 56874
Email: <a class="moz-txt-link-abbreviated" href="mailto:carsten.wolters@uni-muenster.de">carsten.wolters@uni-muenster.de</a>
Web: <a class="moz-txt-link-freetext" href="https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/">https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/</a></pre>
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