brainstorm-tools
update iso2mesh version for ARM
Hello, Iso2mesh was updated to support ARM: https://x.com/FangQ/status/1801795041867776036
This now download iso2mesh directly from github to get this updated version.
Also, it doesnt work if i keep:
% PlugDesc(end).DeleteFiles = {'doc', 'tools', '.git_filters', 'sample', ...
% 'bin/cgalmesh.exe', 'bin/cgalmesh.mexglx', 'bin/cgalmesh.mexmaci', ...
% 'bin/cgalpoly.exe', 'bin/cgalpoly.mexglx', 'bin/cgalpoly.mexmaci', 'bin/cgalpoly.mexa64', 'bin/cgalpoly.mexmaci64', 'bin/cgalpoly_x86-64.exe', ... % Removing cgalpoly completely (not used)
% 'bin/cgalsurf.exe', 'bin/cgalsurf.mexglx', 'bin/cgalsurf.mexmaci', ...
% 'bin/cork.exe', ...
% 'bin/gtsrefine.mexglx', 'bin/gtsrefine.mexmaci', 'bin/gtsrefine.mexarmhf', 'bin/gtsrefine.exe', 'bin/gtsrefine.mexmaci64', ... % Removing gtsrefine completely (not used)
% 'bin/jmeshlib.exe', 'bin/jmeshlib.mexglx', 'bin/jmeshlib.mexmaci', 'bin/jmeshlib.mexmac', 'bin/jmeshlib.mexarmhf', ...
% 'bin/meshfix.exe', 'bin/meshfix.mexglx', 'bin/meshfix.mexmaci', 'bin/meshfix.mexarmhf', ...
% 'bin/tetgen.mexglx', 'bin/tetgen.mexmac', 'bin/tetgen.mexarmhf', ...
% 'bin/tetgen1.5.mexglx'};
% PlugDesc(end).DeleteFilesBin = {'bin/tetgen.exe', 'bin/tetgen.mexa64', 'bin/tetgen.mexmaci', 'bin/tetgen.mexmaci64', 'bin/tetgen_x86-64.exe', ... % Removing older tetgen completely (very sparsely used)
% 'bin/tetgen1.5.exe'};
i get an error with tetgen. But if i dont delete any file, then it works great:
cc: @fangq
how does brainstorm unzip the zip file? using regular unzip, the x permission looks fine.
there is also a possibility of needing xattr -r -d com.apple.quarantine?
~/Downloads$ wget https://github.com/fangq/iso2mesh/archive/refs/heads/master.zip
--2024-07-24 11:51:30-- https://github.com/fangq/iso2mesh/archive/refs/heads/master.zip
Resolving github.com (github.com)... 140.82.112.4
...
~/Downloads$ unzip master.zip
Archive: master.zip
aa78f3a1c9ffdc9dfd41b1ae290161d3233110a5
...
~/Downloads/iso2mesh-master/bin$ ls -lt *mexmaca64
-rwxr-xr-x 1 fangq staff 12766848 Jun 14 16:42 cgalmesh.mexmaca64
-rwxr-xr-x 1 fangq staff 3353160 Jun 14 16:42 cgalsurf.mexmaca64
-rwxr-xr-x 1 fangq staff 488696 Jun 14 16:42 cork.mexmaca64
-rwxr-xr-x 1 fangq staff 324672 Jun 14 16:42 jmeshlib.mexmaca64
-rwxr-xr-x 1 fangq staff 791096 Jun 14 16:42 meshfix.mexmaca64
-rwxr-xr-x 1 fangq staff 810632 Jun 14 16:42 tetgen.mexmaca64
-rwxr-xr-x 1 fangq staff 706776 Jun 14 16:42 tetgen1.5.mexmaca64
how does brainstorm unzip the zip file? using regular unzip, the
xpermission looks fine. there is also a possibility of needingxattr -r -d com.apple.quarantine?~/Downloads$ wget https://github.com/fangq/iso2mesh/archive/refs/heads/master.zip --2024-07-24 11:51:30-- https://github.com/fangq/iso2mesh/archive/refs/heads/master.zip Resolving github.com (github.com)... 140.82.112.4 ... ~/Downloads$ unzip master.zip Archive: master.zip aa78f3a1c9ffdc9dfd41b1ae290161d3233110a5 ... ~/Downloads/iso2mesh-master/bin$ ls -lt *mexmaca64 -rwxr-xr-x 1 fangq staff 12766848 Jun 14 16:42 cgalmesh.mexmaca64 -rwxr-xr-x 1 fangq staff 3353160 Jun 14 16:42 cgalsurf.mexmaca64 -rwxr-xr-x 1 fangq staff 488696 Jun 14 16:42 cork.mexmaca64 -rwxr-xr-x 1 fangq staff 324672 Jun 14 16:42 jmeshlib.mexmaca64 -rwxr-xr-x 1 fangq staff 791096 Jun 14 16:42 meshfix.mexmaca64 -rwxr-xr-x 1 fangq staff 810632 Jun 14 16:42 tetgen.mexmaca64 -rwxr-xr-x 1 fangq staff 706776 Jun 14 16:42 tetgen1.5.mexmaca64
oh actually you are right, permission are fine. Issue i got was because of the file being deleted.
@Edouard2laire, could you identify which removed file(s) are the culprits?
@tmedani, besides the comments in bst_plugin are you familiar with the reasons for removing some files when installing iso2mesh?
@Edouard2laire, could you identify which removed file(s) are the culprits?
i am not sure how. Seems it would require a lot of try and error.
i mainly getting this error:
So i tried to delete everything expet tetgen files, but i still get the same error with the following log file:
------------------------------------------------------------------------
24-Jul-2024 15:16:01 - Running job #1
------------------------------------------------------------------------
24-Jul-2024 15:16:02 - Running 'Segment'
SPM12: spm_preproc_run (v7670) 15:16:02 - 24/07/2024
========================================================================
Segment /Users/edelaire1/.brainstorm/tmp/brain2mesh_240724_151558/sub-01T1.nii,1
Completed : 15:18:25 - 24/07/2024
24-Jul-2024 15:18:25 - Done 'Segment'
24-Jul-2024 15:18:25 - Done
extracting surfaces from a volume ...
region 1 centroid : 144.333333 87.666667 88.500000
processing threshold level 1...
Surface Mesh Extraction Utility (Based on CGAL 5.6.1)
(modified for iso2mesh by Qianqian Fang)
http://iso2mesh.sf.net
RNG seed 1648335518
set initial mesh size to 50
Final number of points: 37761
251 isolated nodes were removed
surface mesh generation is complete
extracting surfaces from a volume ...
region 1 centroid : 139.333333 111.666667 116.500000
processing threshold level 1...
Surface Mesh Extraction Utility (Based on CGAL 5.6.1)
(modified for iso2mesh by Qianqian Fang)
http://iso2mesh.sf.net
RNG seed 1648335518
set initial mesh size to 50
Final number of points: 43898
294 isolated nodes were removed
surface mesh generation is complete
extracting surfaces from a volume ...
region 1 centroid : 142.333333 94.666667 128.500000
processing threshold level 1...
Surface Mesh Extraction Utility (Based on CGAL 5.6.1)
(modified for iso2mesh by Qianqian Fang)
http://iso2mesh.sf.net
RNG seed 1648335518
set initial mesh size to 50
Final number of points: 4125
53 isolated nodes were removed
surface mesh generation is complete
extracting surfaces from a volume ...
region 1 centroid : 131.333333 112.666667 133.500000
processing threshold level 1...
Surface Mesh Extraction Utility (Based on CGAL 5.6.1)
(modified for iso2mesh by Qianqian Fang)
http://iso2mesh.sf.net
RNG seed 1648335518
set initial mesh size to 50
Final number of points: 11710
375 isolated nodes were removed
surface mesh generation is complete
generating tetrahedral mesh from closed surfaces ...
creating volumetric mesh from a surface mesh ...
volume mesh generation is complete
extracting surfaces from a volume ...
region 1 centroid : 102.333333 134.666667 102.000000
processing threshold level 1...
Surface Mesh Extraction Utility (Based on CGAL 5.6.1)
(modified for iso2mesh by Qianqian Fang)
http://iso2mesh.sf.net
RNG seed 1648335518
set initial mesh size to 50
Final number of points: 108985
4593 isolated nodes were removed
surface mesh generation is complete
generating tetrahedral mesh from closed surfaces ...
creating volumetric mesh from a surface mesh ...
volume mesh generation is complete
generating tetrahedral mesh from closed surfaces ...
creating volumetric mesh from a surface mesh ...
volumetric mesh generation failed, returning the intermediate surface model onlyIdleTimeout has been reached.
Here is a more precise error of what happens here: https://github.com/fangq/brain2mesh/blob/master/brain2mesh.m#L361
Error using surf2mesh
Tetgen command failed:
Opening /Users/edelaire1/.brainstorm/tmp/post_vmesh.poly.
Delaunizing vertices...
Delaunay seconds: 1.06491
Creating surface mesh ...
Surface mesh seconds: 0.389386
Constrained Delaunay...
PLC Error: A vertex lies in a segment.
Vertex: [147545] (255.919,158.723,60.1497).
Segment: [147547, 147546] #-1 (0)
A self-intersection was detected. Program stopped.
Hint: use -d option to detect all self-intersections.
Error in s2m (line 35)
[node,elem,face]=surf2mesh(v,f,[],[],keepratio,maxvol,regions,holes,0,method,varargin{:});
i don't understand how not deleting file could solve the issue; so identifying which file to keep is outside of my skill set.
Hey team,
@tmedani, besides the comments in bst_plugin are you familiar with the reasons for removing some files when installing iso2mesh?
we did some tests and selected only the dependencies required by the process_fem_mesh.m I don't understand why this new release is not working; maybe there are some changes in the internal calls for this new release. Is this issue specific to ARM processors?
I agree with @Edouard2laire, testing all the cases with all dependencies can be tedious. Maybe we can just remove those
'doc', 'tools', '.git_filters', 'sample'
and keep all the other files.
@Edouard2laire, could you identify which removed file(s) are the culprits?
i am not sure how. Seems it would require a lot of try and error.
i mainly getting this error: 
if you can share the matlab variables used for the brain2mesh call, I can also take a look
@Edouard2laire, FYI, I tested both built-in examples of brain2mesh on my M2 Mac, and both worked fine.
@Edouard2laire, FYI, I added a missing cgalsimp2 binary for arm64 mac
https://github.com/fangq/iso2mesh/issues/80