A tutorial on fitting data to a series of image 'slices'

Fitting meshes to image data using CMISS


The first thing that one should do before diving in is to look at the shape of the object and decide on how the FE's should be constructed. This will save you a lot of grief in the long run. Since we are going to be fitting a heart we will copy the current Auckland heart, so if you aren't familiar with this you should have a good look at how it is constructed. You can check out CMISS example 1/14/144 or 1/14/147 to get a better look at it if you like.

In summary the FE model of the heart is a hemispherical shape or 'bowl'. The model is composed of two solid FE bowls that are joined together except where the RV occurs. A schematic of this can be seen in the diagram below:

The best way to fit an FE model of the heart (like the above) to image data is to create 3 surfaces or 'bowls' and then link these surfaces together in the Xi3 direction (ie the surfaces are Xi1, Xi2). The three surfaces are:

NOTE: Each of these surfaces must be discretised in a way so that they can be 'hooked up' when we come to create volume elements. ie each surface should have the same number of nodes and elements.

The image data that this mesh is to be fitted to generally comes from a series of MRI slices. Points in space are digitised using the CMISS package to create data clouds of the 3 bowls that we wish to fit the 3 surfaces to.


The basic procedure is:

  1. Digitise the images: This step involves digitising a series of image slices of, e.g, a heart. This will create a 'data cloud' of, say, the epicardial surface which can then have a surface mesh fitted to it.
  2. Creating an initial mesh: One must create an initial mesh that is approximately the same shape as the data. For instance, a half-ellipse is an approximation to the lower half of the surface of the heart.
  3. Fitting the mesh: Having created an initial data cloud and an initial mesh that is an approximation to that cloud, you then have to use cm to fit the nodal parameters of the initial mesh to conform to the data.
  4. Creating the volume elements: Having now fitted surfaces of the epi and endo surfaces you need to link them together to create volume elements.

Examples are:

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