interfaces.slicer.registration.brainsfit

BRAINSFit

Link to code

Wraps command **BRAINSFit **

title: General Registration (BRAINS)

category: Registration

description: Register a three-dimensional volume to a reference volume (Mattes Mutual Information by default). Described in BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, Johnson H.J., Harris G., Williams K., The Insight Journal, 2007. http://hdl.handle.net/1926/1291

version: 3.0.0

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

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

contributor: Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu

acknowledgements: Hans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3); Andriy Fedorov(5) 1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard

Inputs:

[Mandatory]

[Optional]
NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00: (a boolean)
        DO NOT USE THIS FLAG
        flag: --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00
NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01: (a boolean)
        DO NOT USE THIS FLAG
        flag: --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01
NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02: (a boolean)
        DO NOT USE THIS FLAG
        flag: --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02
ROIAutoClosingSize: (a float)
        This flag is only relavent when using ROIAUTO mode for initializing
        masks. It defines the hole closing size in mm. It is rounded up to
        the nearest whole pixel size in each direction. The default is to
        use a closing size of 9mm. For mouse data this value may need to be
        reset to 0.9 or smaller.
        flag: --ROIAutoClosingSize %f
ROIAutoDilateSize: (a float)
        This flag is only relavent when using ROIAUTO mode for initializing
        masks. It defines the final dilation size to capture a bit of
        background outside the tissue region. At setting of 10mm has been
        shown to help regularize a BSpline registration type so that there
        is some background constraints to match the edges of the head
        better.
        flag: --ROIAutoDilateSize %f
args: (a unicode string)
        Additional parameters to the command
        flag: %s
backgroundFillValue: (a float)
        Background fill value for output image.
        flag: --backgroundFillValue %f
bsplineTransform: (a boolean or a file name)
        (optional) Filename to which save the estimated transform. NOTE: You
        must set at least one output object (either a deformed image or a
        transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS BSpline
        flag: --bsplineTransform %s
costFunctionConvergenceFactor: (a float)
         From itkLBFGSBOptimizer.h: Set/Get the
        CostFunctionConvergenceFactor. Algorithm terminates when the
        reduction in cost function is less than (factor * epsmcj) where
        epsmch is the machine precision. Typical values for factor: 1e+12
        for low accuracy; 1e+7 for moderate accuracy and 1e+1 for extremely
        high accuracy. 1e+9 seems to work well.,
        flag: --costFunctionConvergenceFactor %f
costMetric: ('MMI' or 'MSE' or 'NC' or 'MC')
        The cost metric to be used during fitting. Defaults to MMI. Options
        are MMI (Mattes Mutual Information), MSE (Mean Square Error), NC
        (Normalized Correlation), MC (Match Cardinality for binary images)
        flag: --costMetric %s
debugLevel: (an integer (int or long))
        Display debug messages, and produce debug intermediate results.
        0=OFF, 1=Minimal, 10=Maximum debugging.
        flag: --debugLevel %d
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
failureExitCode: (an integer (int or long))
        If the fit fails, exit with this status code. (It can be used to
        force a successfult exit status of (0) if the registration fails due
        to reaching the maximum number of iterations.
        flag: --failureExitCode %d
fixedBinaryVolume: (an existing file name)
        Fixed Image binary mask volume, ONLY FOR MANUAL ROI mode.
        flag: --fixedBinaryVolume %s
fixedVolume: (an existing file name)
        The fixed image for registration by mutual information optimization.
        flag: --fixedVolume %s
fixedVolumeTimeIndex: (an integer (int or long))
        The index in the time series for the 3D fixed image to fit, if
        4-dimensional.
        flag: --fixedVolumeTimeIndex %d
forceMINumberOfThreads: (an integer (int or long))
        Force the the maximum number of threads to use for non thread safe
        MI metric. CAUTION: Inconsistent results my arise!
        flag: --forceMINumberOfThreads %d
gui: (a boolean)
        Display intermediate image volumes for debugging. NOTE: This is not
        part of the standard build sytem, and probably does nothing on your
        installation.
        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. Do NOT use if registering images from
        different modailties.
        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
initialTransform: (an existing file name)
        Filename of transform used to initialize the registration. This CAN
        NOT be used with either CenterOfHeadLAlign, MomentsAlign,
        GeometryAlign, or initialTransform file.
        flag: --initialTransform %s
initializeTransformMode: ('Off' or 'useMomentsAlign' or
         'useCenterOfHeadAlign' or 'useGeometryAlign' or
         'useCenterOfROIAlign')
        Determine how to initialize the transform center. GeometryAlign on
        assumes that the center of the voxel lattice of the images represent
        similar structures. MomentsAlign assumes that the center of mass of
        the images represent similar structures. useCenterOfHeadAlign
        attempts to use the top of head and shape of neck to drive a center
        of mass estimate. Off assumes that the physical space of the images
        are close, and that centering in terms of the image Origins is a
        good starting point. This flag is mutually exclusive with the
        initialTransform flag.
        flag: --initializeTransformMode %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, NearestNeighbor, BSpline, WindowedSinc,
        or ResampleInPlace. The ResampleInPlace option will create an image
        with the same discrete voxel values and will adjust the origin and
        direction of the physical space interpretation.
        flag: --interpolationMode %s
linearTransform: (a boolean or a file name)
        (optional) Filename to which save the estimated transform. NOTE: You
        must set at least one output object (either a deformed image or a
        transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS ---NOT---
        BSpline
        flag: --linearTransform %s
maskInferiorCutOffFromCenter: (a float)
        For use with --useCenterOfHeadAlign (and --maskProcessingMode
        ROIAUTO): the cut-off below the image centers, in millimeters,
        flag: --maskInferiorCutOffFromCenter %f
maskProcessingMode: ('NOMASK' or 'ROIAUTO' or 'ROI')
        What mode to use for using the masks. If ROIAUTO is choosen, then
        the mask is implicitly defined using a otsu forground and hole
        filling algorithm. The Region Of Interest mode (choose ROI) uses the
        masks to define what parts of the image should be used for computing
        the transform.
        flag: --maskProcessingMode %s
maxBSplineDisplacement: (a float)
         Sets the maximum allowed displacements in image physical
        coordinates for BSpline control grid along each axis. A value of 0.0
        indicates that the problem should be unbounded. NOTE: This only
        constrains the BSpline portion, and does not limit the displacement
        from the associated bulk transform. This can lead to a substantial
        reduction in computation time in the BSpline optimizer.,
        flag: --maxBSplineDisplacement %f
maximumStepLength: (a float)
        Internal debugging parameter, and should probably never be used from
        the command line. This will be removed in the future.
        flag: --maximumStepLength %f
medianFilterSize: (a list of items which are an integer (int or
         long))
        The radius for the optional MedianImageFilter preprocessing in all 3
        directions.
        flag: --medianFilterSize %s
minimumStepLength: (a list of items which are a float)
        Each step in the optimization takes steps at least this big. When
        none are possible, registration is complete.
        flag: --minimumStepLength %s
movingBinaryVolume: (an existing file name)
        Moving Image binary mask volume, ONLY FOR MANUAL ROI mode.
        flag: --movingBinaryVolume %s
movingVolume: (an existing file name)
        The moving image for registration by mutual information
        optimization.
        flag: --movingVolume %s
movingVolumeTimeIndex: (an integer (int or long))
        The index in the time series for the 3D moving image to fit, if
        4-dimensional.
        flag: --movingVolumeTimeIndex %d
numberOfHistogramBins: (an integer (int or long))
        The number of histogram levels
        flag: --numberOfHistogramBins %d
numberOfIterations: (a list of items which are an integer (int or
         long))
        The maximum number of iterations to try before failing to converge.
        Use an explicit limit like 500 or 1000 to manage risk of divergence
        flag: --numberOfIterations %s
numberOfMatchPoints: (an integer (int or long))
        the number of match points
        flag: --numberOfMatchPoints %d
numberOfSamples: (an integer (int or long))
        The number of voxels sampled for mutual information computation.
        Increase this for a slower, more careful fit. You can also limit the
        sampling focus with ROI masks and ROIAUTO mask generation.
        flag: --numberOfSamples %d
numberOfThreads: (an integer (int or long))
        Explicitly specify the maximum number of threads to use. (default is
        auto-detected)
        flag: --numberOfThreads %d
outputFixedVolumeROI: (a boolean or a file name)
        The ROI automatically found in fixed image, ONLY FOR ROIAUTO mode.
        flag: --outputFixedVolumeROI %s
outputMovingVolumeROI: (a boolean or a file name)
        The ROI automatically found in moving image, ONLY FOR ROIAUTO mode.
        flag: --outputMovingVolumeROI %s
outputTransform: (a boolean or a file name)
        (optional) Filename to which save the (optional) estimated
        transform. NOTE: You must select either the outputTransform or the
        outputVolume option.
        flag: --outputTransform %s
outputVolume: (a boolean or a file name)
        (optional) Output image for registration. NOTE: You must select
        either the outputTransform or the outputVolume option.
        flag: --outputVolume %s
outputVolumePixelType: ('float' or 'short' or 'ushort' or 'int' or
         'uint' or 'uchar')
        The output image Pixel Type is the scalar datatype for
        representation of the Output Volume.
        flag: --outputVolumePixelType %s
permitParameterVariation: (a list of items which are an integer (int
         or long))
        A bit vector to permit linear transform parameters to vary under
        optimization. The vector order corresponds with transform
        parameters, and beyond the end ones fill in as a default. For
        instance, you can choose to rotate only in x (pitch) with 1,0,0;
        this is mostly for expert use in turning on and off individual
        degrees of freedom in rotation, translation or scaling without
        multiplying the number of transform representations; this trick is
        probably meaningless when tried with the general affine transform.
        flag: --permitParameterVariation %s
projectedGradientTolerance: (a float)
         From itkLBFGSBOptimizer.h: Set/Get the ProjectedGradientTolerance.
        Algorithm terminates when the project gradient is below the
        tolerance. Default lbfgsb value is 1e-5, but 1e-4 seems to work
        well.,
        flag: --projectedGradientTolerance %f
promptUser: (a boolean)
        Prompt the user to hit enter each time an image is sent to the
        DebugImageViewer
        flag: --promptUser
relaxationFactor: (a float)
        Internal debugging parameter, and should probably never be used from
        the command line. This will be removed in the future.
        flag: --relaxationFactor %f
removeIntensityOutliers: (a float)
        The half percentage to decide outliers of image intensities. The
        default value is zero, which means no outlier removal. If the value
        of 0.005 is given, the moduel will throw away 0.005 % of both tails,
        so 0.01% of intensities in total would be ignored in its statistic
        calculation.
        flag: --removeIntensityOutliers %f
reproportionScale: (a float)
        ScaleVersor3D 'Scale' compensation factor. Increase this to put more
        rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern.
        1.0 works well with a translationScale of 1000.0
        flag: --reproportionScale %f
scaleOutputValues: (a boolean)
        If true, and the voxel values do not fit within the minimum and
        maximum values of the desired outputVolumePixelType, then linearly
        scale the min/max output image voxel values to fit within the
        min/max range of the outputVolumePixelType.
        flag: --scaleOutputValues
skewScale: (a float)
        ScaleSkewVersor3D Skew compensation factor. Increase this to put
        more skew in a ScaleSkewVersor3D search pattern. 1.0 works well with
        a translationScale of 1000.0
        flag: --skewScale %f
splineGridSize: (a list of items which are an integer (int or long))
        The number of subdivisions of the BSpline Grid to be centered on the
        image space. Each dimension must have at least 3 subdivisions for
        the BSpline to be correctly computed.
        flag: --splineGridSize %s
strippedOutputTransform: (a boolean or a file name)
        File name for the rigid component of the estimated affine transform.
        Can be used to rigidly register the moving image to the fixed image.
        NOTE: This value is overwritten if either bsplineTransform or
        linearTransform is set.
        flag: --strippedOutputTransform %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: (a list of items which are a unicode string)
        Specifies a list of registration types to be used. The valid types
        are, Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine, and BSpline.
        Specifiying more than one in a comma separated list will initialize
        the next stage with the previous results. If registrationClass flag
        is used, it overrides this parameter setting.
        flag: --transformType %s
translationScale: (a float)
        How much to scale up changes in position compared to unit rotational
        changes in radians -- decrease this to put more rotation in the
        search pattern.
        flag: --translationScale %f
useAffine: (a boolean)
        Perform an Affine registration as part of the sequential
        registration steps. This family of options superceeds the use of
        transformType if any of them are set.
        flag: --useAffine
useBSpline: (a boolean)
        Perform a BSpline registration as part of the sequential
        registration steps. This family of options superceeds the use of
        transformType if any of them are set.
        flag: --useBSpline
useCachingOfBSplineWeightsMode: ('ON' or 'OFF')
        This is a 5x speed advantage at the expense of requiring much more
        memory. Only relevant when transformType is BSpline.
        flag: --useCachingOfBSplineWeightsMode %s
useExplicitPDFDerivativesMode: ('AUTO' or 'ON' or 'OFF')
        Using mode AUTO means OFF for BSplineDeformableTransforms and ON for
        the linear transforms. The ON alternative uses more memory to
        sometimes do a better job.
        flag: --useExplicitPDFDerivativesMode %s
useRigid: (a boolean)
        Perform a rigid registration as part of the sequential registration
        steps. This family of options superceeds the use of transformType if
        any of them are set.
        flag: --useRigid
useScaleSkewVersor3D: (a boolean)
        Perform a ScaleSkewVersor3D registration as part of the sequential
        registration steps. This family of options superceeds the use of
        transformType if any of them are set.
        flag: --useScaleSkewVersor3D
useScaleVersor3D: (a boolean)
        Perform a ScaleVersor3D registration as part of the sequential
        registration steps. This family of options superceeds the use of
        transformType if any of them are set.
        flag: --useScaleVersor3D
writeOutputTransformInFloat: (a boolean)
        By default, the output registration transforms (either the output
        composite transform or each transform component) are written to the
        disk in double precision. If this flag is ON, the output transforms
        will be written in single (float) precision. It is especially
        important if the output transform is a displacement field transform,
        or it is a composite transform that includes several displacement
        fields.
        flag: --writeOutputTransformInFloat
writeTransformOnFailure: (a boolean)
        Flag to save the final transform even if the numberOfIterations are
        reached without convergence. (Intended for use when
        --failureExitCode 0 )
        flag: --writeTransformOnFailure

Outputs:

bsplineTransform: (an existing file name)
        (optional) Filename to which save the estimated transform. NOTE: You
        must set at least one output object (either a deformed image or a
        transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS BSpline
linearTransform: (an existing file name)
        (optional) Filename to which save the estimated transform. NOTE: You
        must set at least one output object (either a deformed image or a
        transform. NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS ---NOT---
        BSpline
outputFixedVolumeROI: (an existing file name)
        The ROI automatically found in fixed image, ONLY FOR ROIAUTO mode.
outputMovingVolumeROI: (an existing file name)
        The ROI automatically found in moving image, ONLY FOR ROIAUTO mode.
outputTransform: (an existing file name)
        (optional) Filename to which save the (optional) estimated
        transform. NOTE: You must select either the outputTransform or the
        outputVolume option.
outputVolume: (an existing file name)
        (optional) Output image for registration. NOTE: You must select
        either the outputTransform or the outputVolume option.
strippedOutputTransform: (an existing file name)
        File name for the rigid component of the estimated affine transform.
        Can be used to rigidly register the moving image to the fixed image.
        NOTE: This value is overwritten if either bsplineTransform or
        linearTransform is set.