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# 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]
    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]
    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 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)
            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 value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    failureExitCode: (an integer)
            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)
            The index in the time series for the 3D fixed image to fit, if
            4-dimensional.
            flag: --fixedVolumeTimeIndex %d
    forceMINumberOfThreads: (an integer)
            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: (an integer)
            The radius for the optional MedianImageFilter preprocessing in all 3
            directions.
            flag: --medianFilterSize %s
    minimumStepLength: (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)
            The index in the time series for the 3D moving image to fit, if
            4-dimensional.
            flag: --movingVolumeTimeIndex %d
    numberOfHistogramBins: (an integer)
            The number of histogram levels
            flag: --numberOfHistogramBins %d
    numberOfIterations: (an integer)
            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)
            the number of match points
            flag: --numberOfMatchPoints %d
    numberOfSamples: (an integer)
            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)
            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: (an integer)
            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: (an integer)
            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
    transformType: (a 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
    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.