Prior Using the Application

1. Deformable Models

You must understand the theory behind deformable models. Specifically, you must understand the parameters and their effect in the final result of segmentation. For additional information refer to publications of Herve Delingette of INRIA, France.

http://www-sop.inria.fr/epidaure/personnel/Herve.Delingette

Just to mention a few

a. Simplex Meshes: a General Representation for 3D Shape Reconstruction.

b. General Object Reconstruction based on Simplex Meshes.

c. Anisotropic Filtering for Model Based Segmentation (Scan-line algorithm), etc.

2. The Initial Model

Deformable models always start from an initial model. There are a few ways to create a model. This application offers you two of them

a. Create a model “sphere” by placing a seed point inside the image.

b. Create a model by providing a binary image “mask” which will be sent to “vtkImageMarchingCubes” for constructing an iso-surface which will then be converted to a Simplex Mesh for deformation.

3. The Image Format

Currently, the application supports meta image format “only”. (i.,e you need to have *.mhd “header” *.raw “image”. Other Image formats will be added in the future.

4. The Image Specifications

Until further changes in the algorithm, only images with spacing (1,1,1) and direction cosine of identity should be used otherwise the results will be incorrect.

5. Visualization

The application provides 4 windows as follows

a. Axial view and slider (Top Left)

b. Coronal view and slider (Top Right)

c. Surface (3D image and Mesh overlayed) (Bottom Left)

d. Sagittal view and slider (Bottom Right)

Guidelines to use the Deformable Model Application

1. Start by bringing up your image (File --> Load Image).

2. Decide which method for creating the initial model.

a. Place a seed point on image “left click”, create Mesh (File --> Create Mesh).

b. Provide binary image (File --> Load Mesh).

3. Create image forces by preprocessing the image (File --> Preprocess Image)

Note Image is send through a few filters before the final Gradient is created.

For further information refer to the parameterization of the filters in the ITK

software guide (segmentation/Level Sets)

anisotropic filtering --> gradient magnitude --> sigmoid --> gradient

4. Check the parameters (Settings --> Segmentation Parameters)

Alpha : Internal Forces (0 < * < 1)

Beta: External Forces ( 0 < * < 1)

Gamma: Damping Force (normally 0.3 < * < 0.4)

Range: Range of Search for Scan line algorithm

Rigidity: Degree of Regularization. (zero will use the 3 immediate neighbors, 1 uses the neighbors and their neighbors and so on).

5. You are now ready for deformation ( Settings --> Deform Mesh)

6. Once you are done deformation you can

a. Save Mesh as “vtkPolyData” (File --> Save Mesh)

b. Save a Mask (i.e, Convert your mesh to a binary image) (File --> Save Mask)