This step is designed for preprocessing 3D binary image data. If your data are surface meshes, you can ignore this step.
In medical imaging domain, many structures of interest are obtained by manual or automated segmentation from volumetric scans (e.g., MRI, CT, etc.), and are often described as 3D binary images. This data preparation step deals with how to remove noises (e.g., 3D holes, bad edge connectivity, bad vertex connectivity, etc) in a 3D binary object so that its voxel surface has a spherical topology. Note that SPHARM-MAT can be used to model arbitrarily shaped but simply connected 3D objects. That is, the object surface needs to have a spherical topology (i.e., genus-zero surface).
If there are small vacancies or discontinuities between image voxels, they can be repaired using the “TopologyFix” tool which will remove any possible sources of error without significantly altering the original image. SPHARM-MAT has two options to do the topology fix: (1) an in-house tool (see Exercise 2.1: In-house Topology Fix for a demo), and (2) an alternative tool integrated from SPHARM-PDM (see Exercise 2.2: SPHARM-PDM Topology Fix for a demo).
This exercise was tested on a WinXP machine (3GHz CPU, 3.25G RAM) running Matlab 7.7.0 (R2008b). It took a few minutes to finish.
Major Steps
Task
Fix the topology of a set of 3D binary objects so that their voxel surfaces have a spherical topology
Input
SpharmMatDir/data/Ex0201/hip01_bim/*_bim.mat
Output
SpharmMatDir/data/Ex0201/hip02_fix/*_fix.mat
Steps
Task
Visualize the binary objects before and after topology fix
Input
SpharmMatDir/data/Ex0201/hip01_bim/*_bim.mat or
SpharmMatDir/data/Ex0201/hip02_fix/*_fix.mat
Output
SpharmMatDir/data/Ex0201/hip01_bim/PNG/*.png or
SpharmMatDir/data/Ex0201/hip02_fix/PNG/*.png
Steps
Notes
Useful Tips
This exercise was tested on a WinXP machine (3GHz CPU, 3.25G RAM) running Matlab 7.7.0 (R2008b) and SPHARM-PDM (WinXP-v1.3). It took a few minutes to finish. In order to run this exercise, you need to install the SPHARM-PDM package (see Install SPHARM-PDM).
Major Steps
Task
Convert matlab 3D binary image format to gipl format used by SPHARM-PDM
Input
SpharmMatDir/data/Ex0202/hip01_bim/*_bim.mat
Output
SpharmMatDir/data/Ex0202/hip02_gipl/*.gipl
Steps
Task
Fix the topology of a set of 3D binary objects so that their voxel surfaces have a spherical topology
Input
SpharmMatDir/data/Ex0202/hip02_gipl/*.gipl
Output
SpharmMatDir/data/Ex0202/hip03_gipl_fix/*_fix.gipl
Steps
Task
Convert gipl format used by SPHARM-PDM to matlab 3D binary image format
Input
SpharmMatDir/data/Ex0202/hip03_gipl_fix/*_fix.gipl
Output
SpharmMatDir/data/Ex0202/hip04_fix/*_fix.mat
Steps
Task
Visualize the binary objects before and after topology fix
Input
SpharmMatDir/data/Ex0202/hip01_bim/*_bim.mat or
SpharmMatDir/data/Ex0202/hip04_fix/*_fix.mat
Output
SpharmMatDir/data/Ex0202/hip01_bim/PNG/*.png or
SpharmMatDir/data/Ex0202/hip04_fix/PNG/*.png
Steps
Notes
Notes
Useful Tips