interfaces.semtools.registration.specialized¶

[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

Release	Devel
0.13.0-rc1	0.13.0-rc1
Download	Github

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interfaces.semtools.registration.specialized¶

BRAINSDemonWarp¶

BRAINSTransformFromFiducials¶

VBRAINSDemonWarp¶