Difference between revisions of "Slicer3:Module:Deformable BSpline registration"

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  [[Documentation|Return to Slicer Documentation]]
 
  [[Documentation|Return to Slicer Documentation]]
  
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This module was implemented by Jim Miller and is based on the ITK b-spline implementation.
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This module was implemented by Jim Miller and Bill Lorensen and is based on the ITK B-spline implementation.
 
*Parameters:
 
*Parameters:
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**Grid Size: smaller number means coarser grid. Higher number means finer grid
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**Iterations: Number of iterations to run the optimization method to estimate the registration parameters.
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**Grid Size: Number of grid points on interior of the fixed image. Larger grid sizes allow for finer registrations.  
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*** You can use this module to manually run a multiresolution registration by starting with a coarse grid, creating a resampled volume, and passing that resampled volume as the moving image for the next run with a finer grid.
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*** '''Make sure you hit the tab key when changing the grid size'''.
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**Histogram bins: Number of histogram bins to use for Mattes Mutual Information. Reduce the number of bins if a deformable registration fails. If the number of bins is too large, the estimated PDFs will be a field of impulses and will inhibit reliable registration estimation.
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**Spatial samples: Number of spatial samples to use in estimating Mattes Mutual Information. Larger values yield more accurate PDFs and improved registration quality.
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**Constrain deformation: Constrain the deformation to the amount specified in Maximum Deformation
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**Maximum deformation: If Constrain Deformation is checked, limit the deformation to this amount.
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**Default pixel value: Default pixel value used if resampling a pixel outside of the volume.
 
*IO
 
*IO
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**Intial Transform: If you ran the affine registration first, you can select that transformation as a start pose
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**Intial Transform: Initial transform for aligning the fixed and moving image. Maps positions in the fixed coordinate frame to positions in the moving coordinate frame. This transform should be an affine or rigid transform.  It is used an a bulk transform for the BSpline. Optional.
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** Output trasnform: is not fully functional yet
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**Fixed image: Fixed image to which to register
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** specify fixed and moving image
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**Moving image: Image to register to the fixed image
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** Output Volume: select create new volume
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** Output transform: Transform calculated that aligns the fixed and moving image. Maps positions from the fixed coordinate frame to the moving coordinate frame. Optional (specify an output transform or an output volume or both).
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** Output Volume: Resampled moving image to fixed image coordinate frame. Optional (specify an output transform or an output volume or both).
 
* click Apply
 
* click Apply
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* Be careful how you set the parameters
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<gallery>
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Image:NoBSpline1.png|Data set that was to be deformed
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Image:WildBSpline.png|Data set after b-Spline with wrong parameters
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</gallery>

Latest revision as of 14:48, 29 October 2008

Home < Slicer3:Module:Deformable BSpline registration
Return to Slicer Documentation

This module was implemented by Jim Miller and Bill Lorensen and is based on the ITK B-spline implementation.

  • Parameters:
    • Iterations: Number of iterations to run the optimization method to estimate the registration parameters.
    • Grid Size: Number of grid points on interior of the fixed image. Larger grid sizes allow for finer registrations.
      • You can use this module to manually run a multiresolution registration by starting with a coarse grid, creating a resampled volume, and passing that resampled volume as the moving image for the next run with a finer grid.
      • Make sure you hit the tab key when changing the grid size.
    • Histogram bins: Number of histogram bins to use for Mattes Mutual Information. Reduce the number of bins if a deformable registration fails. If the number of bins is too large, the estimated PDFs will be a field of impulses and will inhibit reliable registration estimation.
    • Spatial samples: Number of spatial samples to use in estimating Mattes Mutual Information. Larger values yield more accurate PDFs and improved registration quality.
    • Constrain deformation: Constrain the deformation to the amount specified in Maximum Deformation
    • Maximum deformation: If Constrain Deformation is checked, limit the deformation to this amount.
    • Default pixel value: Default pixel value used if resampling a pixel outside of the volume.
  • IO
    • Intial Transform: Initial transform for aligning the fixed and moving image. Maps positions in the fixed coordinate frame to positions in the moving coordinate frame. This transform should be an affine or rigid transform. It is used an a bulk transform for the BSpline. Optional.
    • Fixed image: Fixed image to which to register
    • Moving image: Image to register to the fixed image
    • Output transform: Transform calculated that aligns the fixed and moving image. Maps positions from the fixed coordinate frame to the moving coordinate frame. Optional (specify an output transform or an output volume or both).
    • Output Volume: Resampled moving image to fixed image coordinate frame. Optional (specify an output transform or an output volume or both).
  • click Apply
  • Be careful how you set the parameters

  • Data set that was to be deformed

  • Data set after b-Spline with wrong parameters

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