• Specifications
• ModelAssembly
• ReMappingField

Target Outcome

Define element specific material properties from MRI or CT scan.

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/).

Input

• Tetrahedral mesh of the desired segment region (can include skin, fat, and muscle) (.med format). Use the methods explained in Mesh Generation to build the mesh.

• Labeled (skin, fat, and muscle) image from segmentation (.nii format). Use the methods explained in Image Segmentation to create the labeled image.

Procedures

• SALOME will be used to run the Python script, since it has access to the MEDCoupling library.

  This script converts the image segmentation into a field vector [skin, fat, muscle] for the mesh.

  1. Edit the path to the labeled image.
  2. Edit the path to the mesh.

  3. Choose the nature of the field (Extensive - integrated or Intensive - average) MEDCoupling User Guide - Fields

     • RevIntegral

     • IntegralGlobConstraint

     • ConservativeVolumic

     • Integral
  4. Change the name of the newly created meshes.
  5. Open SALOME and run script.

Output

1. New mesh with associated field to describe the materials of each element (med format). 2. You may also save the source mesh with field (shows the labeled image).

• You can view the mesh with the field in the ParaVis module of SALOME

  1. Once in the ParaVis module, open the .med file that was just created (File>>Open ParaView File)

  2. To visualize the mesh, you may have to click on the eye to the left of the object in the Pipeline Browser.
  3. Under Properties, change the Coloring field to the named field variable (FIELD_trg) and select which tissue to highlight (skin, fat, muscle) from the next drop-down box.
  4. You may also view the mesh by changing the Representation to "Surface With Edges" in the drop-down box right above the Coloring options.

Simple Examples

A simple 16 element hexahedral mesh was formed in the shape of a rectangle to represent the source mesh. This mesh is what would be the image mesh when applying this technique to the Multis project.

Note that the field is split into a vector. One component represents the fat, while the other represents the skin. If the element is skin, the field vector is [1,0] and in the case of fat the field vector is [0,1]. A target mesh is also formed to align with the bottom of the source mesh. The target mesh is a cube, that is half the height of the rectangle. It was split into 6 tetrahedral elements. For this example, we will re-map the hexahedral mesh onto the tetrahedral mesh using the integral interpolation method.

After re-mapping, using the integral method the resulting field appears on the target mesh. Each of the tetrahedral elements partially overlaps 4 different hexahedral elements from the source mesh.

• For element 1, one source element is fat with overlapping volume of 1/6th (0.1667)
• For element 2, three source elements are fat with overlapping volumes of 1/6th, 2/6th, and 1/6th (0.667)
• For element 3, three source elements are skin with overlapping volumes of 3/6th, 3/6th, and 1/6th (1.1667)
• For element 4, two source elements are skin with overlapping volumes of 3/6th and 1/6th (0.667)

Element 1 is the same as element 3, giving a field vector of [1.1667, 0.1667]
Element 2 is the same as element 4, giving a field vector of [0.667, 0.667]