[FieldTrip] tetra volume
Carsten Wolters
carsten.wolters at uni-muenster.de
Thu Apr 1 12:06:16 CEST 2021
Dear Richard,
when I remember right, without having now deeply checked, cstoss is one
of the SimBio-Fortran rountines that is
responsible for the compressed storage of symmetric stiffness matrices
(efficient storage when a matrix has only
few non-zero elements per row, and in FEM it is like that). If it
contains an "empty row", then something went wrong
with building the stiffness matrix. Might you have elements with
zero-conductivity, for example a sinus hole?
Then the simplest solution is that you give those elements low , e.g.
10^-8, conductivity or similar.
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
towards a replacement of the SimBio-FEM with DUNEuro
http://www.duneuro.org/, which is a more up-to-date
C++ code for FEM forward modeling and offers more different FEM options
than SimBio-NeuroFEM, where the latter
only continuous Galerkin-FEM). We currently have a software publication
for DUNEuro in revision, if accepted,
I could send to you.
BR
Carsten
Am 31.03.21 um 18:41 schrieb RICHARDS, JOHN:
>
> I am trying to create a segmented head volume with tetra mesh.
>
> 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.
>
> Then ran the ft_prepare_headmodel with the resulting mesh.
>
> It worked, produced a volume
>
> cfg = [];
>
> cfg.method ='simbio';
>
> cfg.conductivity=conductivity1;
>
> try
>
> vol = ft_prepare_headmodel(cfg, mesh);
>
> catch ME
>
> rethrow(ME)
>
> return;
>
> end
>
> 2—I am trying the same thing now, with the same MRIs and segmenting,
> and etc.
>
> The GUI matlab is running.
>
> STOP Leere Zeile in cstoss is printed in the xterm command line window
>
> The matlab program stops, gives errors like below.
>
> Suggesting it is occurring in the mex file for the simbio mex file.?
>
> 3—I have tried a dozen different combinations of the mesh call to the
> iso2mesh,
>
> [node, elem, face] = vol2mesh(seg, 1:mri.dim(1), 1:mri.dim(2),
> 1:mri.dim(3), 2, 2, isovalue);
>
> isovalues = 0.5;
>
> maxvol=64;
>
> dofix=1;
>
> opt=100;
>
> method='cgalmesh';
>
> ix=[1:mri.dim(1)];
>
> iy=[1:mri.dim(2)];
>
> iz=[1:mri.dim(3)];
>
> img=uint8(seg);
>
> [node,elem,face]=vol2mesh(img,ix,iy,iz,opt,maxvol,dofix,method,isovalues);
>
> [node, elem, face] = vol2mesh(uint8(seg), 1:mri.dim(1), 1:mri.dim(2),
> 1:mri.dim(3), 1, 1, 0, 'cgalmesh');
>
> [node, elem, face] = vol2mesh(uint8(seg), 1:mri.dim(1), 1:mri.dim(2),
> 1:mri.dim(3), isovalues,opt,maxvol, 'cgalmesh');
>
> [node,elem,face]=v2m(uint8(seg),0.5,100,128,method);
>
> [node, elem, face] = vol2mesh(uint8(seg), 1:mri.dim(1), 1:mri.dim(2),
> 1:mri.dim(3), 1, 1, 0, 'cgalmesh');
>
> [node, elem, face] = vol2mesh(uint8(seg), 1:mri.dim(1), 1:mri.dim(2),
> 1:mri.dim(3), 2, 2, 0,'cgalmesh');
>
> 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.
>
> Any ideas?
>
> John
>
> Matlab crash dump
>
> --------------------------------------------------------------------------------
>
> Segmentation violation detected at Wed Mar 31 12:30:03 2021 -0400
>
> --------------------------------------------------------------------------------
>
> Configuration:
>
> Crash Decoding : Disabled - No sandbox or build area path
>
> Crash Mode : continue (default)
>
> Default Encoding : UTF-8
>
> Deployed : false
>
> GNU C Library : 2.17 stable
>
> Graphics Driver : Unknown software
>
> Graphics card 1 : 0x102b ( 0x102b ) 0x533 Version 0.0.0.0
> (0-0-0)
>
> Java Version : Java 1.8.0_202-b08 with Oracle
> Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
>
> MATLAB Architecture : glnxa64
>
> MATLAB Entitlement ID : 4290990
>
> MATLAB Root : /share/apps/MATLAB/R2019b
>
> MATLAB Version : 9.7.0.1190202 (R2019b)
>
> OpenGL : software
>
> Operating System : "CentOS Linux release 7.3.1611 (Core) "
>
> Process ID : 14136
>
> Processor ID : x86 Family 6 Model 79 Stepping 1,
> GenuineIntel
>
> Session Key : 06410f0f-59e8-40e7-b19f-3bbab586464d
>
> Static TLS mitigation : Enabled: Full
>
> Window System : Moba/X (11603000), display localhost:15.0
>
> Fault Count: 1
>
> Abnormal termination:
>
> Segmentation violation
>
> Register State (from fault):
>
> RAX = 00002aaad18c1650 RBX = 00002aaad24e5190
>
> RCX = 00002aaad8db7558 RDX = 0000000000000020
>
> RSP = 00002aaad8db1f38 RBP = 00002aaad8db1fa0
>
> RSI = 0000000000000025 RDI = 00002aaad1941530
>
> R8 = 00002aaac005e060 R9 = 00002aaad000daa0
>
> R10 = 00002aaad8db1d40 R11 = 00002aaaadd45e50
>
> R12 = 00002aaad193ac80 R13 = 0000000000000000
>
> R14 = 0000000000000000 R15 = 000000000000623e
>
> RIP = 00002aaad1997570 EFL = 0000000000010202
>
> CS = 0033 FS = 0000 GS = 0000
>
> Stack Trace (from fault):
>
> [ 0] 0x00002aaad1997570 <unknown-module>+00000000
>
> [ 1] 0x00002aaaabbfd5ee
> /share/apps/MATLAB/R2019b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+01095150
> _ZNSo5flushEv+00000030
>
> [ 2] 0x0000000000000000 <unknown-module>+00000000
>
> This error was detected while a MEX-file was running. If the MEX-file
>
> is not an official MathWorks function, please examine its source code
>
> for errors. Please consult the External Interfaces Guide for information
>
> on debugging MEX-files.
>
> ***********************************************
> John E. Richards
> Carolina Distinguished Professor
> Department of Psychology
> University of South Carolina
> Columbia, SC 29208
> Dept Phone: 803 777 2079
> Fax: 803 777 9558
> Email: richards-john at sc.edu <mailto:richards-john at sc.edu>_
> _https://jerlab.sc.edu
> *************************************************
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
--
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: carsten.wolters at uni-muenster.de
Web: https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/
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