[FieldTrip] tetra volume

Thu Apr 1 12:29:33 CEST 2021

Nein, sondern: P11+P21(angefügt) vs P12+P22(angefügt).

Am 01.04.2021 um 12:06 schrieb Carsten Wolters:
> 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 <https://jerlab.sc.edu>
>> *************************************************
>>
>>
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>> 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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> https://doi.org/10.1371/journal.pcbi.1002202
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