FeaturesIndex.md

xReg Features Index

• Library Features
• Stand-Alone Programs

Library Features:

• Registration:
  • Efficient ray casters for 2D/3D registration and visualization:
    • Line integral (CPU and OpenCL)
    • Line integral approximation via splatting (CPU)
    • Surface rendering (CPU and OpenCL)
    • Depth maps (CPU and OpenCL)
    • Occluding contours (CPU and OpenCL)
    • Sparse collision detection (CPU)
    • Extendable common interface (CPU, OpenCL, and more)
  • Image similarity metrics for driving 2D/3D registrations:
    • Sum of squared differences (SSD) (CPU and OpenCL)
    • Normalized cross correlation (NCC) (CPU and OpenCL)
    • NCC of Sobel Gradients (Grad-NCC) (CPU and OpenCL)
    • Gradient orientation (GO) (CPU)
    • Gradient difference (Grad-Diff) (CPU)
    • Patch-wise NCC (Patch-NCC) (CPU and OpenCL)
    • Patch-wise Grad-NCC (Patch-Grad-NCC) (CPU and OpenCL)
    • Boundary contour distance (CPU)
    • Extendable common interface (CPU, OpenCL, and more)
  • Various optimization strategies for 2D/3D intensity-based registration:
    • CMA-ES
    • Differential Evolution
    • Exhaustive/Grid Search
    • Particle Swarm Optimization
    • Hill Climbing
    • Wrappers around NLOpt routines:
      • BOBYQA
      • CRS
      • DESCH
      • Variations of DIRECT
      • DISRES
      • NEWUOA
      • Nelder Mead
      • PRAXIS
      • Sbplx
    • Extendable common interface
  • Regularizers for 2D/3D intensity-based registration:
    • Rotation and translation magnitudes
    • Euler decomposition magnitudes
    • Rotation and translation magnitudes of relative pose between multiple objects
    • Relative pose difference from nominal AP pose
    • Landmark re-projection distances
    • Heuristics for automatic global pelvis registration
    • Combination of regularizers
    • Extendable common interface
  • Pipeline for chaining together 2D/3D registrations (intensity-based and feature-based) for solving registration problems with multiple-resolutions and views
  • Perspective-n-Point (PnP) solvers (paired point 2D/3D)
    • Minimization of re-projection distances
    • POSIT
    • P3P using C-arm geometry assumptions
    • RANSAC PnP wrapper
  • Paired Point 3D/3D
  • 3D Point Cloud to 3D Surface ICP
• Mesh Processing:
  • Triangular and tetrahedral mesh representations
• Image/Volume Processing:
  • Interpolation of non-uniform spaced slices
  • Image processing operations leveraging lower-level ITK and OpenCV routines
  • Conversion of Hounsfield units (HU) to linear attenuation
  • Poisson noise
  • Image intensity log transform
  • Piecewise rigid volume warping using label maps
• Numerical Optimization:
  • Configurable line search implementation
  • Implementations of several derivative-free methods, including Differential Evolution, Simulated Annealing, and Particle Swarm Optimization
  • Wrapper around C implementation of CMA-ES optimization
  • Suite of test objective functions
• Geometric Primitives and Spatial Data Structures
  • KD-Tree for points or surfaces of arbitrary dimension
  • Primitives with support for intersection, etc.
  • Fitting primitives to data (circle, plane) with robustness to outliers
• Spatial Transformation Utilities:
  • Rotation and rigid transformation utilities, including lie group/algebra routines
  • Perspective projection (3D to 2D)
  • Calculation of anatomical coordinate frames
  • Point cloud manipulation
• Visualization
  • Interactive 3D scene plotting using VTK
• File I/O:
  • Common DICOM fields
  • DICOM files from Siemens CIOS Fusion C-arm
  • Helpers for HDF5 reading/writing
  • Various mesh formats
  • Various image/volume formats (via ITK)
  • 3D Slicer annotations, FCSV and ACSV
  • Comma separated value (CSV) files
• Basic Math Utilities:
  • Basic statistics
  • Distribution fitting
  • Uniformly distributed N-D unit vector sampling
  • Common interface for probability densities and instances for common distributions:
    • Normal
    • Log-normal
    • Folded normal
• General/Common:
  • String parsing/manipulation utilities
  • Serialization streams
  • Command line argument parsing
  • Timer class for measuring runtimes with a stopwatch-like interface
  • Basic filesystem utilities
  • Runtime assertions
• Hip Surgery:
  • Guessing labels of bones from segmentation volumes
  • Planning and modeling of osteotomies
  • Visualization of osteotomies in 3D
  • Modeling of surgical objects, such as screws and K-wires
  • Support for simulated data creation, including randomized screw and K-wire shapes and poses, and volumetric data incorporating osteotomies, repositioned bones, and inserted screws and K-wires

Programs

Some of the capabilities provided by individual programs contained with the apps directory include:

• Image I/O:
  • DICOM conversion and resampling
  • Volume cropping
  • Printing DICOM metadata
• Mesh processing:
  • Mesh creation
  • Mesh display
• Basic point cloud operations:
  • Printing FCSV contents
  • Warping FCSV files
• Registration
  • ICP for 3D point cloud to 3D surface registration
• General utilities for projection data:
  • Advanced visualization of projective geometry coordinate frames with a scene of 3D objects
  • Remap and tile projection data for visualization
  • Tool for creating movie replays of 2D/3D registration processing
  • Extract projection into NIFTY format (.nii/.nii.gz)
  • Insert landmarks (FCSV) into HDF5 projection data
• Hip Surgery: Periacetabular Osteotomy (PAO)
  • Osteotomy planning and modeling
  • Osteotomy 3D visualization
  • Randomized simulation of fragment adjustments
  • Volumetric modeling of fragment adjustments
  • Volumetric modeling of fragment fixation using screws and K-wires
  • Creation of simulated fluoroscopy for 2D/3D registration experiments
  • Examples of 2D/3D, fluoroscopy to CT, registration
    • Single-view pelvis registration
    • Multiple-view, pelvis, femur PAO fragment registration