2008 Summer Project Week:Nonlinear transforms

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MRML scene graph.

Transform node in a MRML scene.

Key Investigators

• GE Research: Jim Miller, Bess Lee
• Isomics: Steve Pieper, Alex Y.

Objective

Extend Slicer's suite of transformations to include nonlinear transformations (B-spline, deformation grids) in the MRML scene, visualization pipeline, and command line modules.

Approach, Plan

• Develop new MRML nodes and MRML storage nodes for B-splines and deformation grids.
  • vtkITK wrapper around ITK classes
• Add attribute to transform nodes to indicate whether they represent a "Transform to World/Parent" or "Transform from World/Parent"
• Extend visualization system for "Transform to World/Parent" or "Transform from World/Parent"
• Extend command line modules to annotate a transformation as a "Transform to World/Parent" or "Transform from World/Parent"
• Identify places in slicer3 code where linear transforms are assumed - these either need generalization or informative warning/error messages

Progress

Concrete

• MRML nodes and storage nodes for B-spline and deformation grids done.
• "Copied" the "Linear registration" module to "Rigid registration"
• "Affine registration" now a shared object library (much faster)

Discussions

• • Eulerian/Langrangian viewpoint discussions
  • Transform file format "should" indicate the coordinate frames and direction a transform maps* "Add Transform..." menu added

Todo

• itkDisplacementFieldTransform
• Transform attribute of coordinate frame
  • Coordinate frame manager from Mike Halle
• Visualization support?
  • TransformDisplayNode?
• Need to patch itkTransformFactory (trunk and release) to register BSplines for 2D and 3D for floats and doubles (Luis)