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# interfaces.slicer.registration.specialized

## ACPCTransform

Link to code

Wraps command **ACPCTransform **

title: ACPC Transform

category: Registration.Specialized

description: <p>Calculate a transformation from two lists of fiducial points.</p><p>ACPC line is two fiducial points, one at the anterior commissure and one at the posterior commissure. The resulting transform will bring the line connecting them to horizontal to the AP axis.</p><p>The midline is a series of points defining the division between the hemispheres of the brain (the mid sagittal plane). The resulting transform will put the output volume with the mid sagittal plane lined up with the AS plane.</p><p>Use the Filtering module<b>Resample Scalar/Vector/DWI Volume</b>to apply the transformation to a volume.</p>

version: 1.0

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ACPCTransform

license: slicer3

contributor: Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)

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]
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    acpc: (a list of from 3 to 3 items which are a float)
            ACPC line, two fiducial points, one at the anterior commissure and
            one at the posterior commissure.
            flag: --acpc %s...
    args: (a string)
            Additional parameters to the command
            flag: %s
    debugSwitch: (a boolean)
            Click if wish to see debugging output
            flag: --debugSwitch
    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
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    midline: (a list of from 3 to 3 items which are a float)
            The midline is a series of points defining the division between the
            hemispheres of the brain (the mid sagittal plane).
            flag: --midline %s...
    outputTransform: (a boolean or a file name)
            A transform filled in from the ACPC and Midline registration
            calculation
            flag: --outputTransform %s

Outputs:

    outputTransform: (an existing file name)
            A transform filled in from the ACPC and Midline registration
            calculation

## BRAINSDemonWarp

Link to code

Wraps command **BRAINSDemonWarp **

title: Demon Registration (BRAINS)

category: Registration.Specialized

description:
  This program finds a deformation field to warp a moving image onto a fixed image. The images must be of the same signal kind, and contain an image of the same kind of object. This program uses the Thirion Demons warp software in ITK, the Insight Toolkit. Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp.

version: 3.0.0

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSDemonWarp

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Hans J. Johnson and Greg Harris.

acknowledgements: The development of this tool was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.

Inputs:

    [Mandatory]
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    arrayOfPyramidLevelIterations: (an integer)
            The number of iterations for each pyramid level
            flag: --arrayOfPyramidLevelIterations %s
    backgroundFillValue: (an integer)
            Replacement value to overwrite background when performing BOBF
            flag: --backgroundFillValue %d
    checkerboardPatternSubdivisions: (an integer)
            Number of Checkerboard subdivisions in all 3 directions
            flag: --checkerboardPatternSubdivisions %s
    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
    fixedBinaryVolume: (an existing file name)
            Mask filename for desired region of interest in the Fixed image.
            flag: --fixedBinaryVolume %s
    fixedVolume: (an existing file name)
            Required: input fixed (target) image
            flag: --fixedVolume %s
    gradient_type: ('0' or '1' or '2')
            Type of gradient used for computing the demons force (0 is
            symmetrized, 1 is fixed image, 2 is moving image)
            flag: --gradient_type %s
    gui: (a boolean)
            Display intermediate image volumes for debugging
            flag: --gui
    histogramMatch: (a boolean)
            Histogram Match the input images. This is suitable for images of the
            same modality that may have different absolute scales, but the same
            overall intensity profile.
            flag: --histogramMatch
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    initializeWithDisplacementField: (an existing file name)
            Initial deformation field vector image file name
            flag: --initializeWithDisplacementField %s
    initializeWithTransform: (an existing file name)
            Initial Transform filename
            flag: --initializeWithTransform %s
    inputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
            Input volumes will be typecast to this format:
            float|short|ushort|int|uchar
            flag: --inputPixelType %s
    interpolationMode: ('NearestNeighbor' or 'Linear' or
             'ResampleInPlace' or 'BSpline' or 'WindowedSinc' or 'Hamming' or
             'Cosine' or 'Welch' or 'Lanczos' or 'Blackman')
            Type of interpolation to be used when applying transform to moving
            volume. Options are Linear, ResampleInPlace, NearestNeighbor,
            BSpline, or WindowedSinc
            flag: --interpolationMode %s
    lowerThresholdForBOBF: (an integer)
            Lower threshold for performing BOBF
            flag: --lowerThresholdForBOBF %d
    maskProcessingMode: ('NOMASK' or 'ROIAUTO' or 'ROI' or 'BOBF')
            What mode to use for using the masks: NOMASK|ROIAUTO|ROI|BOBF. If
            ROIAUTO is choosen, then the mask is implicitly defined using a otsu
            forground and hole filling algorithm. Where the Region Of Interest
            mode uses the masks to define what parts of the image should be used
            for computing the deformation field. Brain Only Background Fill uses
            the masks to pre-process the input images by clipping and filling in
            the background with a predefined value.
            flag: --maskProcessingMode %s
    max_step_length: (a float)
            Maximum length of an update vector (0: no restriction)
            flag: --max_step_length %f
    medianFilterSize: (an integer)
            Median filter radius in all 3 directions. When images have a lot of
            salt and pepper noise, this step can improve the registration.
            flag: --medianFilterSize %s
    minimumFixedPyramid: (an integer)
            The shrink factor for the first level of the fixed image pyramid.
            (i.e. start at 1/16 scale, then 1/8, then 1/4, then 1/2, and finally
            full scale)
            flag: --minimumFixedPyramid %s
    minimumMovingPyramid: (an integer)
            The shrink factor for the first level of the moving image pyramid.
            (i.e. start at 1/16 scale, then 1/8, then 1/4, then 1/2, and finally
            full scale)
            flag: --minimumMovingPyramid %s
    movingBinaryVolume: (an existing file name)
            Mask filename for desired region of interest in the Moving image.
            flag: --movingBinaryVolume %s
    movingVolume: (an existing file name)
            Required: input moving image
            flag: --movingVolume %s
    neighborhoodForBOBF: (an integer)
            neighborhood in all 3 directions to be included when performing BOBF
            flag: --neighborhoodForBOBF %s
    numberOfBCHApproximationTerms: (an integer)
            Number of terms in the BCH expansion
            flag: --numberOfBCHApproximationTerms %d
    numberOfHistogramBins: (an integer)
            The number of histogram levels
            flag: --numberOfHistogramBins %d
    numberOfMatchPoints: (an integer)
            The number of match points for histrogramMatch
            flag: --numberOfMatchPoints %d
    numberOfPyramidLevels: (an integer)
            Number of image pyramid levels to use in the multi-resolution
            registration.
            flag: --numberOfPyramidLevels %d
    numberOfThreads: (an integer)
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputCheckerboardVolume: (a boolean or a file name)
            Genete a checkerboard image volume between the fixedVolume and the
            deformed movingVolume.
            flag: --outputCheckerboardVolume %s
    outputDebug: (a boolean)
            Flag to write debugging images after each step.
            flag: --outputDebug
    outputDisplacementFieldPrefix: (a string)
            Displacement field filename prefix for writing separate x, y, and z
            component images
            flag: --outputDisplacementFieldPrefix %s
    outputDisplacementFieldVolume: (a boolean or a file name)
            Output deformation field vector image (will have the same physical
            space as the fixedVolume).
            flag: --outputDisplacementFieldVolume %s
    outputNormalized: (a boolean)
            Flag to warp and write the normalized images to output. In
            normalized images the image values are fit-scaled to be between 0
            and the maximum storage type value.
            flag: --outputNormalized
    outputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
            outputVolume will be typecast to this format:
            float|short|ushort|int|uchar
            flag: --outputPixelType %s
    outputVolume: (a boolean or a file name)
            Required: output resampled moving image (will have the same physical
            space as the fixedVolume).
            flag: --outputVolume %s
    promptUser: (a boolean)
            Prompt the user to hit enter each time an image is sent to the
            DebugImageViewer
            flag: --promptUser
    registrationFilterType: ('Demons' or 'FastSymmetricForces' or
             'Diffeomorphic')
            Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic
            flag: --registrationFilterType %s
    seedForBOBF: (an integer)
            coordinates in all 3 directions for Seed when performing BOBF
            flag: --seedForBOBF %s
    smoothDisplacementFieldSigma: (a float)
            A gaussian smoothing value to be applied to the deformation feild at
            each iteration.
            flag: --smoothDisplacementFieldSigma %f
    upFieldSmoothing: (a float)
            Smoothing sigma for the update field at each iteration
            flag: --upFieldSmoothing %f
    upperThresholdForBOBF: (an integer)
            Upper threshold for performing BOBF
            flag: --upperThresholdForBOBF %d
    use_vanilla_dem: (a boolean)
            Run vanilla demons algorithm
            flag: --use_vanilla_dem

Outputs:

    outputCheckerboardVolume: (an existing file name)
            Genete a checkerboard image volume between the fixedVolume and the
            deformed movingVolume.
    outputDisplacementFieldVolume: (an existing file name)
            Output deformation field vector image (will have the same physical
            space as the fixedVolume).
    outputVolume: (an existing file name)
            Required: output resampled moving image (will have the same physical
            space as the fixedVolume).

## FiducialRegistration

Link to code

Wraps command **FiducialRegistration **

title: Fiducial Registration

category: Registration.Specialized

description: Computes a rigid, similarity or affine transform from a matched list of fiducials

version: 0.1.0.$Revision$

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/TransformFromFiducials

contributor: Casey B Goodlett (Kitware), Dominik Meier (SPL, BWH)

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]
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    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
    fixedLandmarks: (a list of from 3 to 3 items which are a float)
            Ordered list of landmarks in the fixed image
            flag: --fixedLandmarks %s...
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    movingLandmarks: (a list of from 3 to 3 items which are a float)
            Ordered list of landmarks in the moving image
            flag: --movingLandmarks %s...
    outputMessage: (a string)
            Provides more information on the output
            flag: --outputMessage %s
    rms: (a float)
            Display RMS Error.
            flag: --rms %f
    saveTransform: (a boolean or a file name)
            Save the transform that results from registration
            flag: --saveTransform %s
    transformType: ('Translation' or 'Rigid' or 'Similarity')
            Type of transform to produce
            flag: --transformType %s

Outputs:

    saveTransform: (an existing file name)
            Save the transform that results from registration

## VBRAINSDemonWarp

Link to code

Wraps command **VBRAINSDemonWarp **

title: Vector Demon Registration (BRAINS)

category: Registration.Specialized

description:
  This program finds a deformation field to warp a moving image onto a fixed image. The images must be of the same signal kind, and contain an image of the same kind of object. This program uses the Thirion Demons warp software in ITK, the Insight Toolkit. Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp.

version: 3.0.0

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSDemonWarp

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Hans J. Johnson and Greg Harris.

acknowledgements: The development of this tool was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.

Inputs:

    [Mandatory]
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal
            immediately, `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    arrayOfPyramidLevelIterations: (an integer)
            The number of iterations for each pyramid level
            flag: --arrayOfPyramidLevelIterations %s
    backgroundFillValue: (an integer)
            Replacement value to overwrite background when performing BOBF
            flag: --backgroundFillValue %d
    checkerboardPatternSubdivisions: (an integer)
            Number of Checkerboard subdivisions in all 3 directions
            flag: --checkerboardPatternSubdivisions %s
    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
    fixedBinaryVolume: (an existing file name)
            Mask filename for desired region of interest in the Fixed image.
            flag: --fixedBinaryVolume %s
    fixedVolume: (an existing file name)
            Required: input fixed (target) image
            flag: --fixedVolume %s...
    gradient_type: ('0' or '1' or '2')
            Type of gradient used for computing the demons force (0 is
            symmetrized, 1 is fixed image, 2 is moving image)
            flag: --gradient_type %s
    gui: (a boolean)
            Display intermediate image volumes for debugging
            flag: --gui
    histogramMatch: (a boolean)
            Histogram Match the input images. This is suitable for images of the
            same modality that may have different absolute scales, but the same
            overall intensity profile.
            flag: --histogramMatch
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    initializeWithDisplacementField: (an existing file name)
            Initial deformation field vector image file name
            flag: --initializeWithDisplacementField %s
    initializeWithTransform: (an existing file name)
            Initial Transform filename
            flag: --initializeWithTransform %s
    inputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
            Input volumes will be typecast to this format:
            float|short|ushort|int|uchar
            flag: --inputPixelType %s
    interpolationMode: ('NearestNeighbor' or 'Linear' or
             'ResampleInPlace' or 'BSpline' or 'WindowedSinc' or 'Hamming' or
             'Cosine' or 'Welch' or 'Lanczos' or 'Blackman')
            Type of interpolation to be used when applying transform to moving
            volume. Options are Linear, ResampleInPlace, NearestNeighbor,
            BSpline, or WindowedSinc
            flag: --interpolationMode %s
    lowerThresholdForBOBF: (an integer)
            Lower threshold for performing BOBF
            flag: --lowerThresholdForBOBF %d
    makeBOBF: (a boolean)
            Flag to make Brain-Only Background-Filled versions of the input and
            target volumes.
            flag: --makeBOBF
    max_step_length: (a float)
            Maximum length of an update vector (0: no restriction)
            flag: --max_step_length %f
    medianFilterSize: (an integer)
            Median filter radius in all 3 directions. When images have a lot of
            salt and pepper noise, this step can improve the registration.
            flag: --medianFilterSize %s
    minimumFixedPyramid: (an integer)
            The shrink factor for the first level of the fixed image pyramid.
            (i.e. start at 1/16 scale, then 1/8, then 1/4, then 1/2, and finally
            full scale)
            flag: --minimumFixedPyramid %s
    minimumMovingPyramid: (an integer)
            The shrink factor for the first level of the moving image pyramid.
            (i.e. start at 1/16 scale, then 1/8, then 1/4, then 1/2, and finally
            full scale)
            flag: --minimumMovingPyramid %s
    movingBinaryVolume: (an existing file name)
            Mask filename for desired region of interest in the Moving image.
            flag: --movingBinaryVolume %s
    movingVolume: (an existing file name)
            Required: input moving image
            flag: --movingVolume %s...
    neighborhoodForBOBF: (an integer)
            neighborhood in all 3 directions to be included when performing BOBF
            flag: --neighborhoodForBOBF %s
    numberOfBCHApproximationTerms: (an integer)
            Number of terms in the BCH expansion
            flag: --numberOfBCHApproximationTerms %d
    numberOfHistogramBins: (an integer)
            The number of histogram levels
            flag: --numberOfHistogramBins %d
    numberOfMatchPoints: (an integer)
            The number of match points for histrogramMatch
            flag: --numberOfMatchPoints %d
    numberOfPyramidLevels: (an integer)
            Number of image pyramid levels to use in the multi-resolution
            registration.
            flag: --numberOfPyramidLevels %d
    numberOfThreads: (an integer)
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputCheckerboardVolume: (a boolean or a file name)
            Genete a checkerboard image volume between the fixedVolume and the
            deformed movingVolume.
            flag: --outputCheckerboardVolume %s
    outputDebug: (a boolean)
            Flag to write debugging images after each step.
            flag: --outputDebug
    outputDisplacementFieldPrefix: (a string)
            Displacement field filename prefix for writing separate x, y, and z
            component images
            flag: --outputDisplacementFieldPrefix %s
    outputDisplacementFieldVolume: (a boolean or a file name)
            Output deformation field vector image (will have the same physical
            space as the fixedVolume).
            flag: --outputDisplacementFieldVolume %s
    outputNormalized: (a boolean)
            Flag to warp and write the normalized images to output. In
            normalized images the image values are fit-scaled to be between 0
            and the maximum storage type value.
            flag: --outputNormalized
    outputPixelType: ('float' or 'short' or 'ushort' or 'int' or 'uchar')
            outputVolume will be typecast to this format:
            float|short|ushort|int|uchar
            flag: --outputPixelType %s
    outputVolume: (a boolean or a file name)
            Required: output resampled moving image (will have the same physical
            space as the fixedVolume).
            flag: --outputVolume %s
    promptUser: (a boolean)
            Prompt the user to hit enter each time an image is sent to the
            DebugImageViewer
            flag: --promptUser
    registrationFilterType: ('Demons' or 'FastSymmetricForces' or
             'Diffeomorphic' or 'LogDemons' or 'SymmetricLogDemons')
            Registration Filter Type: Demons|FastSymmetricForces|Diffeomorphic|L
            ogDemons|SymmetricLogDemons
            flag: --registrationFilterType %s
    seedForBOBF: (an integer)
            coordinates in all 3 directions for Seed when performing BOBF
            flag: --seedForBOBF %s
    smoothDisplacementFieldSigma: (a float)
            A gaussian smoothing value to be applied to the deformation feild at
            each iteration.
            flag: --smoothDisplacementFieldSigma %f
    upFieldSmoothing: (a float)
            Smoothing sigma for the update field at each iteration
            flag: --upFieldSmoothing %f
    upperThresholdForBOBF: (an integer)
            Upper threshold for performing BOBF
            flag: --upperThresholdForBOBF %d
    use_vanilla_dem: (a boolean)
            Run vanilla demons algorithm
            flag: --use_vanilla_dem
    weightFactors: (a float)
            Weight fatctors for each input images
            flag: --weightFactors %s

Outputs:

    outputCheckerboardVolume: (an existing file name)
            Genete a checkerboard image volume between the fixedVolume and the
            deformed movingVolume.
    outputDisplacementFieldVolume: (an existing file name)
            Output deformation field vector image (will have the same physical
            space as the fixedVolume).
    outputVolume: (an existing file name)
            Required: output resampled moving image (will have the same physical
            space as the fixedVolume).