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# nipype.interfaces.slicer.registration.brainsfit module

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## BRAINSFit

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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

> NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00a boolean

>   DO NOT USE THIS FLAG. Maps to a command-line argument: `--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00`.

> NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01a boolean

>   DO NOT USE THIS FLAG. Maps to a command-line argument: `--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01`.

> NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02a boolean

>   DO NOT USE THIS FLAG. Maps to a command-line argument: `--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02`.

> ROIAutoClosingSizea 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. Maps to a command-line argument: `--ROIAutoClosingSize %f`.

> ROIAutoDilateSizea 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. Maps to a command-line argument: `--ROIAutoDilateSize %f`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> backgroundFillValuea float

>   Background fill value for output image. Maps to a command-line argument: `--backgroundFillValue %f`.

> bsplineTransforma boolean or a pathlike object or string representing a file

>   (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. Maps to a command-line argument: `--bsplineTransform %s`.

> costFunctionConvergenceFactora 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., .

>   Maps to a command-line argument: `--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). Maps to a command-line argument: `--costMetric %s`.

> debugLevelan integer (int or long)

>   Display debug messages, and produce debug intermediate results. 0=OFF, 1=Minimal, 10=Maximum debugging. Maps to a command-line argument: `--debugLevel %d`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> failureExitCodean 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. Maps to a command-line argument: `--failureExitCode %d`.

> fixedBinaryVolumea pathlike object or string representing an existing file

>   Fixed Image binary mask volume, ONLY FOR MANUAL ROI mode. Maps to a command-line argument: `--fixedBinaryVolume %s`.

> fixedVolumea pathlike object or string representing an existing file

>   The fixed image for registration by mutual information optimization. Maps to a command-line argument: `--fixedVolume %s`.

> fixedVolumeTimeIndexan integer (int or long)

>   The index in the time series for the 3D fixed image to fit, if 4-dimensional. Maps to a command-line argument: `--fixedVolumeTimeIndex %d`.

> forceMINumberOfThreadsan integer (int or long)

>   Force the the maximum number of threads to use for non thread safe MI metric. CAUTION: Inconsistent results my arise!. Maps to a command-line argument: `--forceMINumberOfThreads %d`.

> guia boolean

>   Display intermediate image volumes for debugging. NOTE: This is not part of the standard build sytem, and probably does nothing on your installation. Maps to a command-line argument: `--gui`.

> histogramMatcha 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. Maps to a command-line argument: `--histogramMatch`.

> initialTransforma pathlike object or string representing an existing file

>   Filename of transform used to initialize the registration. This CAN NOT be used with either CenterOfHeadLAlign, MomentsAlign, GeometryAlign, or initialTransform file. Maps to a command-line argument: `--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. Maps to a command-line argument: `--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. Maps to a command-line argument: `--interpolationMode %s`.

> linearTransforma boolean or a pathlike object or string representing a file

>   (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. Maps to a command-line argument: `--linearTransform %s`.

> maskInferiorCutOffFromCentera float

>   For use with –useCenterOfHeadAlign (and –maskProcessingMode ROIAUTO): the cut-off below the image centers, in millimeters, . Maps to a command-line argument: `--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. Maps to a command-line argument: `--maskProcessingMode %s`.

> maxBSplineDisplacementa 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., .

>   Maps to a command-line argument: `--maxBSplineDisplacement %f`.

> maximumStepLengtha float

>   Internal debugging parameter, and should probably never be used from the command line. This will be removed in the future. Maps to a command-line argument: `--maximumStepLength %f`.

> medianFilterSizea list of items which are an integer (int or long)

>   The radius for the optional MedianImageFilter preprocessing in all 3 directions. Maps to a command-line argument: `--medianFilterSize %s`.

> minimumStepLengtha 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. Maps to a command-line argument: `--minimumStepLength %s`.

> movingBinaryVolumea pathlike object or string representing an existing file

>   Moving Image binary mask volume, ONLY FOR MANUAL ROI mode. Maps to a command-line argument: `--movingBinaryVolume %s`.

> movingVolumea pathlike object or string representing an existing file

>   The moving image for registration by mutual information optimization. Maps to a command-line argument: `--movingVolume %s`.

> movingVolumeTimeIndexan integer (int or long)

>   The index in the time series for the 3D moving image to fit, if 4-dimensional. Maps to a command-line argument: `--movingVolumeTimeIndex %d`.

> numberOfHistogramBinsan integer (int or long)

>   The number of histogram levels. Maps to a command-line argument: `--numberOfHistogramBins %d`.

> numberOfIterationsa 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. Maps to a command-line argument: `--numberOfIterations %s`.

> numberOfMatchPointsan integer (int or long)

>   The number of match points. Maps to a command-line argument: `--numberOfMatchPoints %d`.

> numberOfSamplesan 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. Maps to a command-line argument: `--numberOfSamples %d`.

> numberOfThreadsan integer (int or long)

>   Explicitly specify the maximum number of threads to use. (default is auto-detected). Maps to a command-line argument: `--numberOfThreads %d`.

> outputFixedVolumeROIa boolean or a pathlike object or string representing a file

>   The ROI automatically found in fixed image, ONLY FOR ROIAUTO mode. Maps to a command-line argument: `--outputFixedVolumeROI %s`.

> outputMovingVolumeROIa boolean or a pathlike object or string representing a file

>   The ROI automatically found in moving image, ONLY FOR ROIAUTO mode. Maps to a command-line argument: `--outputMovingVolumeROI %s`.

> outputTransforma boolean or a pathlike object or string representing a file

>   (optional) Filename to which save the (optional) estimated transform. NOTE: You must select either the outputTransform or the outputVolume option. Maps to a command-line argument: `--outputTransform %s`.

> outputVolumea boolean or a pathlike object or string representing a file

>   (optional) Output image for registration. NOTE: You must select either the outputTransform or the outputVolume option. Maps to a command-line argument: `--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. Maps to a command-line argument: `--outputVolumePixelType %s`.

> permitParameterVariationa 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. Maps to a command-line argument: `--permitParameterVariation %s`.

> projectedGradientTolerancea 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., .

>   Maps to a command-line argument: `--projectedGradientTolerance %f`.

> promptUsera boolean

>   Prompt the user to hit enter each time an image is sent to the DebugImageViewer. Maps to a command-line argument: `--promptUser`.

> relaxationFactora float

>   Internal debugging parameter, and should probably never be used from the command line. This will be removed in the future. Maps to a command-line argument: `--relaxationFactor %f`.

> removeIntensityOutliersa 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. . Maps to a command-line argument: `--removeIntensityOutliers %f`.

> reproportionScalea 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. Maps to a command-line argument: `--reproportionScale %f`.

> scaleOutputValuesa 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. Maps to a command-line argument: `--scaleOutputValues`.

> skewScalea 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. Maps to a command-line argument: `--skewScale %f`.

> splineGridSizea 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. . Maps to a command-line argument: `--splineGridSize %s`.

> strippedOutputTransforma boolean or a pathlike object or string representing a file

>   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. Maps to a command-line argument: `--strippedOutputTransform %s`.

> transformTypea 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. Maps to a command-line argument: `--transformType %s`.

> translationScalea 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. Maps to a command-line argument: `--translationScale %f`.

> useAffinea 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. Maps to a command-line argument: `--useAffine`.

> useBSplinea 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. Maps to a command-line argument: `--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. Maps to a command-line argument: `--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. Maps to a command-line argument: `--useExplicitPDFDerivativesMode %s`.

> useRigida 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. Maps to a command-line argument: `--useRigid`.

> useScaleSkewVersor3Da 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. Maps to a command-line argument: `--useScaleSkewVersor3D`.

> useScaleVersor3Da 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. Maps to a command-line argument: `--useScaleVersor3D`.

> writeOutputTransformInFloata 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. Maps to a command-line argument: `--writeOutputTransformInFloat`.

> writeTransformOnFailurea boolean

>   Flag to save the final transform even if the numberOfIterations are reached without convergence. (Intended for use when –failureExitCode 0 ). Maps to a command-line argument: `--writeTransformOnFailure`.

> bsplineTransforma pathlike object or string representing an existing file

>   (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.

> linearTransforma pathlike object or string representing an existing file

>   (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.

> outputFixedVolumeROIa pathlike object or string representing an existing file

>   The ROI automatically found in fixed image, ONLY FOR ROIAUTO mode.

> outputMovingVolumeROIa pathlike object or string representing an existing file

>   The ROI automatically found in moving image, ONLY FOR ROIAUTO mode.

> outputTransforma pathlike object or string representing an existing file

>   (optional) Filename to which save the (optional) estimated transform. NOTE: You must select either the outputTransform or the outputVolume option.

> outputVolumea pathlike object or string representing an existing file

>   (optional) Output image for registration. NOTE: You must select either the outputTransform or the outputVolume option.

> strippedOutputTransforma pathlike object or string representing an existing file

>   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.