Breast Phantom Generation

This document summarizes the whole pipeline, from CT images to compressed breast phantoms, by means of a FEM simulation.

The algorithm is divided into 3 main parts:

• Biomechanical model construction
• FEM simulation - i.e. breast compression
• Image (i.e. phantom) reconstruction.

Dependencies

This software was written using c++ and, mainly, the itk and vtk libraries.

⚠️ Currently, the software uses vtk v.7 (i.e. datafile version v.2). However, the latest vtk version v.9 uses another file datafile version (v.5.1), and it may affect to the performance. I'm checking this issue

The biomechanical model extraction is performed using the library iso2mesh and, therefore, we need to use either Matlab$^{TM}$ or Octave$^{TM}$. We are trying a code based on the cgal library to directly transform itk images into 3D meshes.

The FE compression is performed using NiftySim v.2.5.1.

⚠️ This is the most important but the most outdated part.

NiftySim and the reconstruction algorithm uses CUDA, to speed up the process.

Current situation

The current code was not directly written to create bCT phantoms but as a part of a multimodal registration pipeline. Therefore, it may fail in several parts.

Currently, I'm Checking and sharing the code.

Pipeline

Biomechanical Model/Rewrite Information

Convert breast.tiff images into breast.nrrdimages

./RewriteInformation breast_segmentation.tiff output_path.nrrd voxelSizeX voxelSizeY voxelSizeZ

• output:
  • breast_image.nrrd original breast segmentation image with spacial information
  • resampled_image.nrrd breast mask with $0.273\times0.273\times0.273~mm^3$

Biomechanical Model/Matlab Code

Biomechanical model extraction using iso2mesh.

⚠️ Check the folder!

• output:
  • mesh.vtk Contains the FE breast model (with boundary Conditions and element labels???)

FE Simulation/Write Nifty Model

Function WriteNiftyModel writes a .xml file to perform the FE simulation using NiftySim. Some arguments are defined as default. I should improve this

./WriteNiftyModel <biomechanical-mesh.vtk> <breast-image.nrrd> <path-to-nifitysim-model.xml> <breast-thickness>

• inputs:

  • biomechanical-mesh.vtk or mesh.vtkobtained from the previous step
  • breast-image.nrrd obtained from the first step
  • path-to-niftysim-model.xml
  • breast-thickness

• output:

  • niftysim-model.xml

Support +20 mm

Paddle BB-20-thickness (check!)

NiftySim usage:

./niftysim -x <path-to-niftysim-model.xml> -v -t -sport -export-mesh <path-to-output-mesh.vtk>

• arguments:

  • -v verbose
  • -t print time
  • -sport GPU (MANDATORY)
  • -export-mesh

• output:

  • output-mesh.vtk

The output .vtk mesh contains the node displacement as cell data. The newest vtk version may affect this step and the following.

Phantom Reconstruction/Reconstruct Image

Function ReconstructImage perform the final ...

./ReconstructImage <path-to-niftysim-output-mesh.vtk> <path-to-breast-image.nrrd> <output-compressed-breast-mesh.vtk> <output-phantom-image.nrrd> 

• output
  • compressed-breast-mesh.vtk
  • phantom-image.nrrd