Elastix, The Manual Elastix V4.7

• 1 Introduction
  • 1.1 Outline of this manual
  • 1.2 Quick start
  • 1.3 Acknowledgements
• 2 Image registration
  • 2.1 Registration framework
  • 2.2 Images
  • 2.3 Metrics
  • 2.4 Image samplers
  • 2.5 Interpolators
  • 2.6 Transforms
  • 2.7 Optimisers
  • 2.8 Multi-resolution
    • 2.8.1 Data complexity
    • 2.8.2 Transformation complexity
  • 2.9 Evaluating registration
  • 2.10 Visualizing registration
• 3 elastix
  • 3.1 Introduction
    • 3.1.1 Key features
  • 3.2 Getting started
    • 3.2.1 Getting started the really easy way
    • 3.2.2 Getting started the easy way
  • 3.3 How to call elastix
  • 3.4 The parameter file
• 4 transformix
  • 4.1 Introduction
  • 4.2 How to call transformix
  • 4.3 The transform parameter file
  • 4.4 Some details
    • 4.4.1 Run-time
    • 4.4.2 Memory consumption
• 5 Tutorial
  • 5.1 Selecting the registration components
  • 5.2 Overview of all parameters
  • 5.3 Important parameters
    • 5.3.1 Registration
    • 5.3.2 Metric
    • 5.3.3 Sampler
    • 5.3.4 Interpolator
    • 5.3.5 Transform
    • 5.3.6 Optimiser
    • 5.3.7 Image pyramids
  • 5.4 Masks
  • 5.5 Trouble shooting
    • 5.5.1 Common errors
    • 5.5.2 Bad initial alignment
    • 5.5.3 Memory consumption
• 6 Advanced topics
  • 6.1 Metrics
    • 6.1.1 Image registration with multiple metrics and/or images
    • 6.1.2 -mutual information
    • 6.1.3 Penalty terms
    • 6.1.4 Bending energy penalty
    • 6.1.5 Rigidity penalty
    • 6.1.6 DisplacementMagnitudePenalty: inverting transformations
    • 6.1.7 Corresponding points: help the registration
    • 6.1.8 VarianceOverLastDimensionMetric: aligning time series
  • 6.2 Image samplers
  • 6.3 Interpolators
  • 6.4 Transforms
  • 6.5 Optimisation methods
• 7 Developers guide
  • 7.1 Relation to ITK
  • 7.2 Overview of the elastix code
    • 7.2.1 Directory structure
  • 7.3 Using elastix in your own software
    • 7.3.1 Including elastix code in your own software
    • 7.3.2 Using elastix as a library
  • 7.4 Creating new components
  • 7.5 Coding style
• A Example parameter file
• B Example transform parameter file
• C Practical exercise: using VV with elastix
  • C.1 Manual rigid registration
  • C.2 Automated rigid registration
  • C.3 Non-rigid registration
• D Software License
• Bibliography