Documentation/Nightly/Extensions/ScatteredTransform

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For the stable Slicer documentation, visit the 4.8 page.


Introduction and Acknowledgements

Extension: ScatteredTransform
Acknowledgments: G. R. Joldes has been funded by Raine Medical Research Foundation through a Raine Priming Grant.
Author: G. R. Joldes

Module Description

Creates a BSpline transform from a displacement field defined at scattered points by using the Multi-level BSpline interpolation algorithm.


Use Cases

1. Create a B-Spline transform based on two sets of fiducials.

2. Create a B-Spline transform based on two sets of points read from files. These files can contain the initial and deform configurations for a biomechanics-based FEM or mesh-free registration. The resulting B-Spline transform can be used to warp 3D images, a process which is very time consuming if spatial interpolation is performed using the mesh [1]. This module reduces the image warping time from hours to seconds.

Brain shift computed using a biomechanics based brain model and FEM. The deformed high resolution pre-operative image (left) is compared to the intra-operative image (right). The pre-operative image has been warped using the B-Spline obtained by applying ScatteredTransform to the original and deformed mesh nodal positions.
A section through the brain computational model used to predict the brain shift, showing the ventricles (green) and tumor (red).

Panels and their use

Module UI
Advanced parameters
    Input points:
  • Initial landmarks: Ordered list of fiducials in initial position. Select these from the moving image if the resulting transform is used for image registration.
  • Displaced landmarks: Ordered list of fiducials in displaced position. Select these from the fixed image if the resulting transform is used for image registration.
  • Input files:

  • File with initial point positions: File with coordinates of points in initial position.
  • File with displaced point positions: File with coordinates of points in displaced position.
  • Ignore first value: Ignores first value in each line of the input files (which may be a node number).
  • Output transform:

  • Slicer BSpline Transform: Slicer transform node for the generated B-Spline transform. NOTE: Only 3D transforms are handled by 3D Slicer!
  • Advanced parameters:

  • BSpline Transform file: File where to save the transform. Needed for 1D and 2D transforms, as Slicer does not create a transform node for these transforms.
  • Space dimension: The space dimension (1D, 2D or 3D).
  • For use in: Where is the transform going to be used? If the transform is a 3D transform to be used in Slicer, a coordinate transformation (similar to what Slicer does internally) is applied to the coordinates before the transform is computed.(only 3D transforms can be used in Slicer)
  • Invert transform: Inverts the transform. Always done if transform is for use in Slicer.
  • Use linear approximation: Sets the initial B-Spline grid values using a linear approximation of the displacements.
  • B-Spline Grid Spacing: The distance between the BSpline control grid points.
  • Domain computed from input points: Computes the transform domain as the bounding box of the input points.
  • Minimum domain coordinates: The minimum coordinates of the domain (if not computed from input points).
  • Maximum domain coordinates: The maximum coordinates of the domain (if not computed from input points).
  • Tolerance: Absolute tolerance in approximating the transform at the input points.
  • Minimum grid spacing: Minimum grid spacing during grid refinement.
  • Maximum number of levels: Maximum number of levels of B-Spline refinements.
  • Output information:

  • Residual: Display residual approximation error on successful completion.

References

1. Joldes GR, Wittek A, Warfield SK, Miller K (2012) "Performing Brain Image Warping Using the Deformation Field Predicted by a Biomechanical Model." In: Nielsen PMF, Miller K, Wittek A, editors. Computational Biomechanics for Medicine: Deformation and Flow: Springer New York. pp. 89-96.