[FieldTrip] tetra volume

[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
*************************************************

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