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Calculate Atrial Volume

Table of contents

  1. Background
  2. QuickStart
  3. Dependencies
    1. Compiling fillholes
  4. Process
    1. Close holes with FileHoles
    2. Convert the VTP file to a STL file
    3. Calculate the Volume in MeshLab
  5. Publications using this code

Background

Segmentation tools, including CEMRG often output cardiac chamber geometries as manifolds with holes representing anatomic structures. To calculate the volume of these structures, we first post-process these manifolds to close any existing holes. Subsequently, we calculate the volume contained within the structure.

QuickStart

system('source ~/.bash_profile'); % ensure relevant folders are on the path
hVtk = VTKReader('openfile');
system(['FillHoles ' hVtk.Filename ' 1000000']);
% if there are still holes, then
system(['FillHoles ~/Desktop/FillHolesOutput.vtk 1000000']);
hVtk = VTKReader('~/Desktop/FillHolesOutput.vtk');
hVtk.readAllData();
hVtk.writeStl();

/Applications/meshlab.app/Contents/MacOS/meshlabserver -i ~/Desktop/FillHolesOutput.stl -s ~/Documents/Dropbox/Matlab_Code/librarysteven/meshlabserver/untitled.mlx

Dependencies

  • VTK
  • VTK FillHoles filter (see compilation instructions below)
  • Paraview
  • Meshlab

Compiling fillholes

FillHoles is available from here. Alternatively, clone this version to allow the user to specify the size of holes.

git clone https://github.com/drsewilliams/fillholes.git ./fillholes
cd fillholes/build
cmake ..
make

For ease, copy the executable to a location on your path (fillholes/build/FillHoles.app/Contents/MacOS/FillHoles).

Process

Close holes with FileHoles

FillHoles input.vtk 1000000

A window will appear showing the original mesh and the ‘filled holes’ version. It may be there are still holes. In which case, the input parameter 100000 may need to be increased. The output will be saved to the desktop as FillHolesOutput.vtp.

It is possible that you will have to run FillHoles on the mesh more than once. In which case:

Fileholes ~/Desktop/FileHolesOutput.vtp 1000000

Convert the VTP file to a STL file

Using Paraview, open the new VTP file. Use Save Data to save the file as an STL file.

Calculate the Volume in MeshLab

In MeshLab, import the STL mesh. Using the Compute Geometrics filter, calculate the volume. The volume will be displayed in the output console: e.g. “Mesh Volume 38297”. If you cannot see the output console, go to View > Show Layer Dialog

Publications using this code