Difference between revisions of "Documentation/Nightly/Extensions/ScatteredTransform"

From Slicer Wiki
Jump to: navigation, search
 
(3 intermediate revisions by the same user not shown)
Line 28: Line 28:
 
2. Create a B-Spline transform based on two sets of points read from files.  
 
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.  
 
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].
+
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_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.]]
Line 43: Line 43:
 
|}
 
|}
 
<UL>
 
<UL>
<LI>Initial landmarks: </LI>
+
<strong>Input points:</strong>
 +
<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>
 +
<strong>Input files:</strong>
 +
<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>
 +
<strong>Output transform:</strong>
 +
<LI>Slicer BSpline Transform: Slicer transform node for the generated B-Spline transform. NOTE: Only 3D transforms are handled by 3D Slicer!</LI>
 +
<strong>Advanced parameters:</strong>
 +
<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>
 +
<strong>Output information:</strong>
 +
<LI>Residual: Display residual approximation error on successful completion.</LI>
 
</UL>
 
</UL>
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
Line 53: Line 76:
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-footer}}
 
{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]
+
[[Category:Documentation/{{documentation/version}}/Extensions]]
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->

Latest revision as of 06:19, 3 March 2017

Home < Documentation < Nightly < Extensions < ScatteredTransform


For the latest Slicer documentation, visit the read-the-docs.


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.