Target Outcome

A finite element mesh of a tissue of interest ready for model development with:

node definitions
element definitions
node set definitions
element set definitions
surface set definitions

Protocols

Required Infrastructure

SALOME is an open-source software that provides a generic platform for pre- (cad, meshing) and post-processing for numerical simulation (LGPL license, see http://www.salome-platform.org/).
Gmsh is a free 3D finite element grid generator with a build-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. (GNU General Public License (GPL license, see http://gmsh.info/)

Input

Surface representation of tissue of interest; in Stl format in MRI coordinate system .

For more details, see Geometry Generation.

Procedures

SALOME will be used as the primary meshing tool for Multis.

Automated

SALOME has an advanced python interface that allows access to all of its functionality. Installing this into python is quite difficult. However running a script in SALOME is easy! Just open SALOME and select File > Load Script. Browse to the file and open.

This python script will take an xml file with the connectivity of several stl files in the same coordinate system. It will then mesh them in 3D, and create groups of elements and nodes for applying boundary conditions. Currently it makes groups of all, outer surface, and a proximity based tie condition.

Instructions for running the script and creating the xml input file can be found here.

Learn how to easily add python libraries to Salome here.

Manual

Start SALOME and select the Mesh module, when the activate module dialog comes up select New.
Import the stl surface using File > Import > STL file. When the file loads, it may not draw it to the screen. Click the eye icon next to the file name to toggle visibility. (Visibility is not required to complete this procedure.)
Right click the file and select Edit Mesh/Sub-mesh.
While staying on the default 3D tab change the Algorithm drop down to Tetrahedron (Netgen), then click Apply and Close.
Right click on the file again and select Compute. A window will appear showing information on the computed mesh, click Close.
Right click the file and select Create Group and create the desired groups.
Export the resulting mesh File > Export > UNV file (or other format).

Gmsh

Gmsh is a much lighter meshing program. If you don't require the might of SALOME you might consider this for 3D mesh an stl.

Make a new Gmsh geo file with these lines.

Merge 'StlFileOfInterest.stl';
SL = newreg;    Surface Loop(SL) = {1};
V = newv;       Volume(V) = {SL};
Physical Volume('MeaningfulName', 1) = {V};
Mesh 3;

Get the desired groups by setting them manually.

Then File > Save As... and select your format.

If it doesn't mesh

Sometimes the stl might be bad and these procedures won't work. Here's how to fix it.

Output

Volumetric finite element mesh of tissue of interest; in still to be determined format

node definitions (numbering and coordinates)
element definitions (numbering, element-specific node numbers and connectivity)
node set definitions (set name(s) and relevant node numbers)
element set definitions (set name(s) and relevant element numbers)
face definitions (numbering, face-specific node numbers and connectivity)
surface set definitions (set name(s) and relevant face numbers)

The completed finite element mesh output is used in Model Assembly.

To assign material properties to the mesh from a labeled image, see Re-mapping Field.