#Build gmsh linux install
#Build gmsh linux manual
#Build gmsh linux registration

Make: Leaving directory `/var/tmp/portage/sci-libs/gmsh-2.2.5/work/gmsh-2.2.5/contrib/MathEval' I'm experiencing build failures with USE=-metis. usr/lib/libcgns.so(cg_coord_write+0x305) usr/lib/libcgns.so(ADFH_Write_All_Data+0x25) Info : 'gmsh -2 -o t6.cgns -format cgns t6.geo' started on Mon Jul 14 23:43:17 2008 ~/tutorial $ gmsh -2 -o t6.cgns -format cgns t6.geo I have no clue if it is related to cgnslibs, hdf5, gmsh or ebuild itself. *** glibc detected *** gmsh: free(): invalid next size (fast): 0x083b31a0 *** Info : 'gmsh -2 -o t6.cgns -format cgns t6.geo ' started on Sat Mar 22 13:58:13 2008 Info : Increasing process stack size (8192 kB < 16 MB) ~/tutorial$ gmsh -2 -o t6.cgns -format cgns t6.geo This ebuild has no problem to build with cgns, but cgns write failed: probably configure should check the cgns dependency on hdf5, this issue should be reported upstream (I will do it). if cgns is built with hdf5 backend for data storage, it needs -lhdf5 link flag to work correctly, I made a crude fix in configure.

#Build gmsh linux install

introduced examples USE flag to install demos and tutorial filesĢ. When something goes wrong, you can check the m2m_ subID /headreco_log.html file.Vesion bump + cgns fix for hdf5 backend + examples USE flagġ.

Subject space is defined by the qform set in the m2m_ subID / subID _T1fs_, which can be found in the same folder as the head mesh. The transformations are stored in the m2m_ subID /toMNI/ directory.

#Build gmsh linux registration

The transformation is based on a non-linear whole-head registration of the T1 of the subject to the MNI template that is determined during the SPM12 segmentation procedure. Please see below for a description of the corresponding command line programs. Transformation from and to MNI space: Both positions and results such as the electric field can be transformed between MNI and subject space. For now, these surfaces cannot be manually improved. Note: When using CAT12, surfaces instead of voxel masks will be stored for GM and WM in the mask_prep/ folder.

$build gmsh linux$

Add -no-cat to the surfacemesh step in case you did nott use CAT12. Then run headreco surfacemesh subID and headreco volumemesh subID to re-create the head mesh based on the edited masks.

#Build gmsh linux manual

Manual editing: Edit one or more of the binary masks stored in m2m_ subID /mask_prep/. As a standard, headreco uses 0.5 nodes per mm², resulting in head meshes with around 4 million tetrahedra.Īfter the head mesh creation, temporary files are deleted to save disk space. Mesh resolution can be controlled using the -v option, which allows setting the vertex density (nodes per mm²) of the surface meshes.