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# interfaces.slicer.registration.brainsfit

## BRAINSFit

Link to code

Wraps command **/home/raid3/gorgolewski/software/slicer/Slicer –launch 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
    NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01: (a boolean)
            DO NOT USE THIS FLAG
    NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02: (a boolean)
            DO NOT USE THIS FLAG
    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.
    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.
    args: (a string)
            Additional parameters to the command
    backgroundFillValue: (a float)
            Background fill value for output image.
    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
    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.,
    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)
    debugLevel: (an integer)
            Display debug messages, and produce debug intermediate results.  0=OFF, 1=Minimal,
            10=Maximum debugging.
    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.
    fixedBinaryVolume: (an existing file name)
            Fixed Image binary mask volume, ONLY FOR MANUAL ROI mode.
    fixedVolume: (an existing file name)
            The fixed image for registration by mutual information optimization.
    fixedVolumeTimeIndex: (an integer)
            The index in the time series for the 3D fixed image to fit, if 4-dimensional.
    forceMINumberOfThreads: (an integer)
            Force the the maximum number of threads to use for non thread safe MI metric.  CAUTION:
            Inconsistent results my arise!
    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.
    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.
    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.
    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.
    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.
    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
    maskInferiorCutOffFromCenter: (a float)
            For use with --useCenterOfHeadAlign (and --maskProcessingMode ROIAUTO): the cut-off
            below the image centers, in millimeters,
    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.
    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.,
    maximumStepLength: (a float)
            Internal debugging parameter, and should probably never be used from the command line.
            This will be removed in the future.
    medianFilterSize: (an integer)
            The radius for the optional MedianImageFilter preprocessing in all 3 directions.
    minimumStepLength: (a float)
            Each step in the optimization takes steps at least this big.  When none are possible,
            registration is complete.
    movingBinaryVolume: (an existing file name)
            Moving Image binary mask volume, ONLY FOR MANUAL ROI mode.
    movingVolume: (an existing file name)
            The moving image for registration by mutual information optimization.
    movingVolumeTimeIndex: (an integer)
            The index in the time series for the 3D moving image to fit, if 4-dimensional.
    numberOfHistogramBins: (an integer)
            The number of histogram levels
    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
    numberOfMatchPoints: (an integer)
            the number of match points
    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.
    numberOfThreads: (an integer)
            Explicitly specify the maximum number of threads to use. (default is auto-detected)
    outputFixedVolumeROI: (a boolean or a file name)
            The ROI automatically found in fixed image, ONLY FOR ROIAUTO mode.
    outputMovingVolumeROI: (a boolean or a file name)
            The ROI automatically found in moving image, ONLY FOR ROIAUTO mode.
    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.
    outputVolume: (a boolean or a file name)
            (optional) Output image for registration. NOTE: You must select either the
            outputTransform or the outputVolume option.
    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.
    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.
    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.,
    promptUser: (a boolean)
            Prompt the user to hit enter each time an image is sent to the DebugImageViewer
    relaxationFactor: (a float)
            Internal debugging parameter, and should probably never be used from the command line.
            This will be removed in the future.
    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.
    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
    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.
    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
    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.
    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.
    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.
    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.
    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.
    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.
    useCachingOfBSplineWeightsMode: ('ON' or 'OFF')
            This is a 5x speed advantage at the expense of requiring much more memory.  Only
            relevant when transformType is BSpline.
    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.
    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.
    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.
    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.
    writeTransformOnFailure: (a boolean)
            Flag to save the final transform even if the numberOfIterations are reached without
            convergence. (Intended for use when --failureExitCode 0 )

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.