Modules:RegisterImages-Documentation-3.4

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Module Name

MyModule

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General Information

Module Type & Category

Type: CLI Module calling ITK functions

Category: Registration

Authors, Collaborators & Contact

• Author1: Stephen Aylward, Kitware
• Contributor1: Ron Kikinis (documentation)
• Contact: name, email

Module Description

This Module is an integrated framework providing access to ITK registration technologies. Algorithms can be run in single mode or pipelined. Depending on the size of the data sets, a significant amount of memory is needed. There is an option to trade off speed for memory. Most of the code is parallelized and will take advantage of multicore capabilities, if available.

Major Features

The major features of the module include:

• Default parameters register many full-head and skull-stripped MRI: rigid, affine, and BSpline
• Offers a complete, pipeline-based registration solution
  • Load and apply existing transforms
  • Compute rigid, affine, and bspline transforms in sequence with a single command
• Intuitive parameters
  • Instead of setting obscure "scales" for parameters, you set global values for "Expected Offset", "Expected Rotation", ... to indicate how much mis-registration is anticipated in the data being registered
• MinimizeMemory option provides a way to compute bspline registrations using a dense set of control points and a large number of samples on "normal" computers (albeit computation time increases)
• SampleFromOverlap option allows images of vastly different sizes to be registered
  • Helps to avoid (but does not completely eliminate) the annoying ITK exception, "too many samples falls outside of the image"
• Incorporates testing
  • Specify a baseline image, and modules will perform the requested registration, compare its results with the baseline image, and return success/failure
• Based on an extensible and re-usable class structure.

Usage

Examples, Use Cases & Tutorials

• Note use cases for which this module is especially appropriate, and/or link to examples.
• Link to examples of the module's use
• Link to any existing tutorials

Quick Tour of Features and Use

See here for more information.

Main Registration Panel

The module implements a registration pipeline. The steps in that pipeline are as follows:

• Step 1: Loaded transform
  • You may load a pre-computed transform to initialize the registration.
  • If one is loaded, it is immediately applied (i.e., the moving image is resampled)
• Step 2: Initial registration
  • Options are:
    • None (sets the center of rotation to the center of the moving image)
    • Landmark (uses N-pairs of landmarks (passed as vectors) and a least-squared error metric to register the images using a rigid transform
    • Image Centers (shifts the images to align their centers)
    • Centers of Mass (shifts the images to align their centers of mass)
    • Second Moments (shifts and rotates the images to align the 1st and 2nd moments)
• Step 3: Registration
  • Options are:
    • None (applies the loaded transforms)
    • Initial
      • computes and applies the initial transform to the loaded registrations)
    • Rigid
      • computes a rigid transform and then applies it to the loaded registrations
    • Affine
      • computes an affine transform and then applies it to the loaded registrations
    • BSpline
      • computes a bspline transform and then applies it to the loaded registrations
    • PipelineRigid
      • computes a rigid transform (initialized using the results from the initial registration) and then applies it to the loaded registrations
    • PipelineAffine
      • computes a rigid transform (initialized using the results from the initial registration), uses those results to initialize and compute an affine transform, and then applies it to the loaded registrations
    • PipelineBSpline
      • computes a rigid transform (initialized using the results from the initial registration), uses those results to initialize and compute an affine transform, and then applies it to the loaded registrations, THEN computes and applies a BSpline transform

• 

  IO panel
  Resample image is the resampled moving image.

• 

  Global Parameters
  This panel controls what will happen. You can choose to have one of the algorithms run or to pipeline several of them together.

• 

  Advanced Global Parameters

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  Testing Parameters

• 

  Initialization of rigid registration

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  Advanced Parameters for rigid registration

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  Advanced Parameters for affine registration

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  Advanced Parameters for B-Spline registration

Development

Dependencies

Other modules or packages that are required for this module's use.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Customize following links for your module.

Links to documentation generated by doxygen.

More Information

Acknowledgment

Include funding and other support here.

References

Publications related to this module go here. Links to pdfs would be useful.