UpdateBot: Nightly -> 4.10

2018-10-19T00:44:48Z

Nightly -> 4.10

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Extension: [[Documentation/{{documentation/version}}/Extensions/ScatteredTransform|ScatteredTransform]] 
Acknowledgments:
G. R. Joldes has been funded by Raine Medical Research Foundation through a Raine Priming Grant. 
Author: G. R. Joldes

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{{documentation/{{documentation/version}}/module-section|Module Description}}

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


{{documentation/{{documentation/version}}/module-section|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.
{|
|[[Image:ScatteredTransform_displacementField.png|thumb|340px|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.]]
|[[Image:ScatteredTransform_mesh.jpg|thumb|200px|A section through the brain computational model used to predict the brain shift, showing the ventricles (green) and tumor (red).]]
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}

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|[[Image:ScatteredTransform_panel.png|thumb|560px|Module UI]]
|[[Image:ScatteredTransform_panelAdvanced.png|thumb|560px|Advanced parameters]]
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<UL>
Input points:
<LI>Initial landmarks: Ordered list of fiducials in initial position. Select these from the moving image if the resulting transform is used for image registration.</LI>
<LI>Displaced landmarks: Ordered list of fiducials in displaced position. Select these from the fixed image if the resulting transform is used for image registration.</LI>
Input files:
<LI>File with initial point positions: File with coordinates of points in initial position.</LI>
<LI>File with displaced point positions: File with coordinates of points in displaced position.</LI>
<LI>Ignore first value: Ignores first value in each line of the input files (which may be a node number).</LI>
Output transform:
<LI>Slicer BSpline Transform: Slicer transform node for the generated B-Spline transform. NOTE: Only 3D transforms are handled by 3D Slicer!</LI>
Advanced parameters:
<LI>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.</LI>
<LI>Space dimension: The space dimension (1D, 2D or 3D).</LI>
<LI>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)</LI>
<LI>Invert transform: Inverts the transform. Always done if transform is for use in Slicer.</LI>
<LI>Use linear approximation: Sets the initial B-Spline grid values using a linear approximation of the displacements.</LI>
<LI>B-Spline Grid Spacing: The distance between the BSpline control grid points.</LI>
<LI>Domain computed from input points: Computes the transform domain as the bounding box of the input points.</LI>
<LI>Minimum domain coordinates: The minimum coordinates of the domain (if not computed from input points).</LI>
<LI>Maximum domain coordinates: The maximum coordinates of the domain (if not computed from input points).</LI>
<LI>Tolerance: Absolute tolerance in approximating the transform at the input points.</LI>
<LI>Minimum grid spacing: Minimum grid spacing during grid refinement.</LI>
<LI>Maximum number of levels: Maximum number of levels of B-Spline refinements.</LI>
Output information:
<LI>Residual: Display residual approximation error on successful completion.</LI>
</UL>

{{documentation/{{documentation/version}}/module-section|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.


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UpdateBot: Nightly -> 4.10