interfaces.semtools.registration.specialized

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://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSDemonWarp.

version: 3.0.0

documentation-url: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/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]

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
arrayOfPyramidLevelIterations: (a list of items which are an integer
         (int or long))
        The number of iterations for each pyramid level
        flag: --arrayOfPyramidLevelIterations %s
backgroundFillValue: (an integer (int or long))
        Replacement value to overwrite background when performing BOBF
        flag: --backgroundFillValue %d
checkerboardPatternSubdivisions: (a list of items which are an
         integer (int or long))
        Number of Checkerboard subdivisions in all 3 directions
        flag: --checkerboardPatternSubdivisions %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 (int or long))
        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: (a list of items which are an integer (int or
         long))
        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: (a list of items which are an integer (int or
         long))
        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: (a list of items which are an integer (int or
         long))
        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: (a list of items which are an integer (int or
         long))
        neighborhood in all 3 directions to be included when performing BOBF
        flag: --neighborhoodForBOBF %s
numberOfBCHApproximationTerms: (an integer (int or long))
        Number of terms in the BCH expansion
        flag: --numberOfBCHApproximationTerms %d
numberOfHistogramBins: (an integer (int or long))
        The number of histogram levels
        flag: --numberOfHistogramBins %d
numberOfMatchPoints: (an integer (int or long))
        The number of match points for histrogramMatch
        flag: --numberOfMatchPoints %d
numberOfPyramidLevels: (an integer (int or long))
        Number of image pyramid levels to use in the multi-resolution
        registration.
        flag: --numberOfPyramidLevels %d
numberOfThreads: (an integer (int or long))
        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 unicode 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: (a list of items which are an integer (int or long))
        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
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
upFieldSmoothing: (a float)
        Smoothing sigma for the update field at each iteration
        flag: --upFieldSmoothing %f
upperThresholdForBOBF: (an integer (int or long))
        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).

BRAINSTransformFromFiducials

Link to code

Wraps command ** BRAINSTransformFromFiducials **

title: Fiducial Registration (BRAINS)

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://www.slicer.org/slicerWiki/index.php/Modules:TransformFromFiducials-Documentation-3.6

contributor: Casey B Goodlett

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]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
fixedLandmarks: (a list of items which are a list of from 3 to 3
         items which are a float)
        Ordered list of landmarks in the fixed image
        flag: --fixedLandmarks %s...
fixedLandmarksFile: (an existing file name)
        An fcsv formatted file with a list of landmark points.
        flag: --fixedLandmarksFile %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 items which are a list of from 3 to 3
         items which are a float)
        Ordered list of landmarks in the moving image
        flag: --movingLandmarks %s...
movingLandmarksFile: (an existing file name)
        An fcsv formatted file with a list of landmark points.
        flag: --movingLandmarksFile %s
numberOfThreads: (an integer (int or long))
        Explicitly specify the maximum number of threads to use.
        flag: --numberOfThreads %d
saveTransform: (a boolean or a file name)
        Save the transform that results from registration
        flag: --saveTransform %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
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://www.slicer.org/slicerWiki/index.php/Documentation/4.1/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]

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
arrayOfPyramidLevelIterations: (a list of items which are an integer
         (int or long))
        The number of iterations for each pyramid level
        flag: --arrayOfPyramidLevelIterations %s
backgroundFillValue: (an integer (int or long))
        Replacement value to overwrite background when performing BOBF
        flag: --backgroundFillValue %d
checkerboardPatternSubdivisions: (a list of items which are an
         integer (int or long))
        Number of Checkerboard subdivisions in all 3 directions
        flag: --checkerboardPatternSubdivisions %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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: (a list of items which are 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 (int or long))
        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: (a list of items which are an integer (int or
         long))
        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: (a list of items which are an integer (int or
         long))
        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: (a list of items which are an integer (int or
         long))
        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: (a list of items which are an existing file name)
        Required: input moving image
        flag: --movingVolume %s...
neighborhoodForBOBF: (a list of items which are an integer (int or
         long))
        neighborhood in all 3 directions to be included when performing BOBF
        flag: --neighborhoodForBOBF %s
numberOfBCHApproximationTerms: (an integer (int or long))
        Number of terms in the BCH expansion
        flag: --numberOfBCHApproximationTerms %d
numberOfHistogramBins: (an integer (int or long))
        The number of histogram levels
        flag: --numberOfHistogramBins %d
numberOfMatchPoints: (an integer (int or long))
        The number of match points for histrogramMatch
        flag: --numberOfMatchPoints %d
numberOfPyramidLevels: (an integer (int or long))
        Number of image pyramid levels to use in the multi-resolution
        registration.
        flag: --numberOfPyramidLevels %d
numberOfThreads: (an integer (int or long))
        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 unicode 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: (a list of items which are an integer (int or long))
        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
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
upFieldSmoothing: (a float)
        Smoothing sigma for the update field at each iteration
        flag: --upFieldSmoothing %f
upperThresholdForBOBF: (an integer (int or long))
        Upper threshold for performing BOBF
        flag: --upperThresholdForBOBF %d
use_vanilla_dem: (a boolean)
        Run vanilla demons algorithm
        flag: --use_vanilla_dem
weightFactors: (a list of items which are 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).