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interfaces.slicer.legacy.registration

AffineRegistration

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/legacy/registration.py#L75

Wraps command ** AffineRegistration **

title: Fast Affine registration

category: Legacy.Registration

description: Registers two images together using an affine transform and mutual information. This module is often used to align images of different subjects or images of the same subject from different modalities.

This module can smooth images prior to registration to mitigate noise and improve convergence. Many of the registration parameters require a working knowledge of the algorithm although the default parameters are sufficient for many registration tasks.

version: 0.1.0.$Revision: 18864 $(alpha)

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Modules/AffineRegistration

contributor: Daniel Blezek

acknowledgements: This module was developed by Daniel Blezek while at GE Research with contributions from Jim Miller.

This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Inputs:

[Mandatory]

[Optional]
FixedImageFileName: (an existing file name)
        Fixed image to which to register
MovingImageFileName: (an existing file name)
        Moving image
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
fixedsmoothingfactor: (an integer)
        Amount of smoothing applied to fixed image prior to registration. Default is 0 (none).
        Range is 0-5 (unitless). Consider smoothing the input data if there is considerable
        amounts of noise or the noise pattern in the fixed and moving images is very different.
histogrambins: (an integer)
        Number of histogram bins to use for Mattes Mutual Information. Reduce the number of bins
        if a 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.
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
initialtransform: (an existing file name)
        Initial transform for aligning the fixed and moving image.  Maps positions in the fixed
        coordinate frame to positions in the moving coordinate frame. Optional.
iterations: (an integer)
        Number of iterations
movingsmoothingfactor: (an integer)
        Amount of smoothing applied to moving image prior to registration. Default is 0 (none).
        Range is 0-5 (unitless). Consider smoothing the input data if there is considerable
        amounts of noise or the noise pattern in the fixed and moving images is very different.
outputtransform: (a boolean or a file name)
        Transform calculated that aligns the fixed and moving image. Maps positions in the fixed
        coordinate frame to the moving coordinate frame. Optional (specify an output transform
        or an output volume or both).
resampledmovingfilename: (a boolean or a file name)
        Resampled moving image to the fixed image coordinate frame. Optional (specify an output
        transform or an output volume or both).
spatialsamples: (an integer)
        Number of spatial samples to use in estimating Mattes Mutual Information. Larger values
        yield more accurate PDFs and improved registration quality.
translationscale: (a float)
        Relative scale of translations to rotations, i.e. a value of 100 means 10mm = 1 degree.
        (Actual scale used is 1/(TranslationScale^2)). This parameter is used to "weight" or
        "standardized" the transform parameters and their effect on the registration objective
        function.

Outputs:

outputtransform: (an existing file name)
        Transform calculated that aligns the fixed and moving image. Maps positions in the fixed
        coordinate frame to the moving coordinate frame. Optional (specify an output transform
        or an output volume or both).
resampledmovingfilename: (an existing file name)
        Resampled moving image to the fixed image coordinate frame. Optional (specify an output
        transform or an output volume or both).

BSplineDeformableRegistration

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/legacy/registration.py#L31

Wraps command ** BSplineDeformableRegistration **

title: Fast Nonrigid BSpline registration

category: Legacy.Registration

description: Registers two images together using BSpline transform and mutual information.

version: 0.1.0.$Revision: 18864 $(alpha)

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Modules/BSplineDeformableRegistration

contributor: Bill Lorensen

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Inputs:

[Mandatory]

[Optional]
FixedImageFileName: (an existing file name)
        Fixed image to which to register
MovingImageFileName: (an existing file name)
        Moving image
args: (a string)
        Additional parameters to the command
constrain: (a boolean)
        Constrain the deformation to the amount specified in Maximum Deformation
default: (an integer)
        Default pixel value used if resampling a pixel outside of the volume.
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
gridSize: (an integer)
        Number of grid points on interior of the fixed image. Larger grid sizes allow for finer
        registrations.
histogrambins: (an integer)
        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.
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
initialtransform: (an existing file name)
        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.
iterations: (an integer)
        Number of iterations
maximumDeformation: (a float)
        If Constrain Deformation is checked, limit the deformation to this amount.
outputtransform: (a boolean or a file name)
        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).
outputwarp: (a boolean or a file name)
        Vector field that applies an equivalent warp as the BSpline. Maps positions from the
        fixed coordinate frame to the moving coordinate frame. Optional.
resampledmovingfilename: (a boolean or a file name)
        Resampled moving image to fixed image coordinate frame. Optional (specify an output
        transform or an output volume or both).
spatialsamples: (an integer)
        Number of spatial samples to use in estimating Mattes Mutual Information. Larger values
        yield more accurate PDFs and improved registration quality.

Outputs:

outputtransform: (an existing file name)
        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).
outputwarp: (an existing file name)
        Vector field that applies an equivalent warp as the BSpline. Maps positions from the
        fixed coordinate frame to the moving coordinate frame. Optional.
resampledmovingfilename: (an existing file name)
        Resampled moving image to fixed image coordinate frame. Optional (specify an output
        transform or an output volume or both).