brains:Namespaces

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Contents 1 Brains::itk Namespace 1.1 AndImage 1.2 GradientAnisotropicDiffusion 1.3 CastImage 1.4 ClipImage 1.5 ConnectedComponentImage 1.6 GrayscaleFillhole 1.7 ImageMath 1.8 ConstantImageMath 1.9 NaryMaximumImageFilter 1.10 NaryAddImageFilter 1.11 ComputeImageMean 1.12 ImageRegion 1.13 IntensityWindowingImage 1.14 LargestRegionFilledMask 1.15 LoadImage 1.16 MaskImage 1.17 measureVolumeLabelImage 1.18 measureLabelImageStatistics 1.19 MedianImageFilter 1.20 NotImage 1.21 NotImage 1.22 NotImage 1.23 ResampleImage 1.24 ResampleImageWithReferenceImage 1.25 RescaleImage 1.26 SaveImage 1.27 ShiftScaleImage 1.28 SignedDistanceImage 1.29 JointCommonMaskEstimationFromSTAPLEFilter 1.30 ThresholdImage 1.31 BinaryThresholdImage 2 Brains::itkUtils namespace 2.1 convertBrainsDataTypeStringToItk 2.2 getItkImageType 2.3 GetImageMin 2.4 GetImageMax 2.5 GetItkImageSize 2.6 GetItkImageSpacing 2.7 GetItkImageOrigin 2.8 readItkTransform 2.9 WriteItkTransform 3 Brains::External Namespace 3.1 runConvertImageType 3.2 runClipInferior 3.3 runACPCDetect 3.4 runRigidRegistration 3.5 runClipROIAUTO 3.6 runMaskROIAUTO 3.7 runBRAINSFit 3.8 runBrainsMush 3.9 runKmeansClassification 3.10 runRandomSampleClassPlugs 3.11 runRandomSampleClassPlugs 3.12 runBRAINSClassify 3.13 runBRAINSDiscreteClass 3.14 runN4ITK 3.15 runBayesianClassification 3.16 runBiasCorrector 3.17 runCreateTalairachParameters 3.18 runCreateTalairachMask 3.19 runBRAINSDemonsWarp 3.20 runApplyWarp 3.21 runFullBRAINSABC 3.22 runSimpleEM 3.23 runBrainsCortex 3.24 runBRAINSApplySurfaceLabels 3.25 runBRAINSMeasureSurface

Brains::itk Namespace

AndImage

• Usage: AndImage inputImage1 inputImage2
• Description: Preform logical AND of two images. The images should be an integral type. The user provides two images for the operation and the resulting image that is returned will be the same type as the first image

GradientAnisotropicDiffusion

• GradientAnisotropicDiffusion {inputImage {conductance 1} {rmsError 1} }
  • TEST

CastImage

• Usage: CastImage inputImage outputDataType
• Description: Cast an image from its current data type to the specified output type.
• Output Types:
  • Unsigned-8bit
  • Signed-16bit
  • Unsigned-32bit
  • Float-single
• NOTE: We are in the process of also supporting the wrap ITK strings UC3, SS3, UL3, and F3

ClipImage

• Usage: ClipImage inputImage clipRegion ?backgroundValue?
• Description: Retain the rectangular region specified by clipRegion from an image. Clip region must be valid itkRegion. The resulting image will have the same size, origin, and spacing as the original image. The default backgroundValue value is 0.

ConnectedComponentImage

• Usage: ConnectedComponentImage inputImage ?fullyConnected? ?outputDataType?
• Description: Labels objects in a binary image. Each Object is assigned a unique label. The resulting object labels start with 1 and are consecutive. fullyConnected strictly enforces face connectivity versus face+edge+vertex connectivity. The default is face+edge+vertex connectivity. The default outputDataType is Unsigned-32bit. This is the only output data-type supported and is a current limitation in wrapping.

GrayscaleFillhole

• Usage: GrayscaleFillhole inputImage ?fullyConnected?
• Description: Fill holes in a greyscale image. fullyConnected should be either On or Off.

ImageMath

• Usage: ImageMath inputImage1 inputImage2 operation ?outputDataType?
  • Description: Perform the specified math operation between the two images provided. The valid operations are:
  • Add
  • Subtract
  • Multiply
  • Divide

By default the output image type is the same as the first image. The user can specify the output data-type. See CastImage for a list of valid data-types.

ConstantImageMath

• Usage: ConstantImageMath inputImage constant operation
• Description: Perform the specified math operation between an image and the specified constant value. The valid operations are:
  • Add
  • Subtract
  • Multiply
  • Divide

NaryMaximumImageFilter

• Usage: NaryMaximumImageFilter inputImageList
• Description: Compute the maximum value voxel-by-voxel from a list of images. It can also be used to quickly generate a labelmap of non-overlapping regions if you are willing to accept the numerical hierarchy that is imposed.

NaryAddImageFilter

• Usage: NaryAddImageFilter inputImageList ?outputDataType?
• Description: Add together N images specified in the image list. It is expected that all of the inout images have the same image type. The user can specify the output data-type. See CastImage for a list of valid data-types. The default output type is the same as the images.

ComputeImageMean

• Usage: ComputeImageMean inputImageList ?outputDataType?
• Description:Compute the voxel-by-voxel mean from the image list. It is expected that all of the input images have the same image type. The user can specify the output data-type. See CastImage for a list of valid data-types. The default output type is the same as the images.

ImageRegion

• Usage: ImageRegion dimensions size index
• Description: Defines a region of interest, i.e. itkImageRegion. The dimensions define the number of dimensions (2 or 3). size and index are lists of dimension size that define the Size and Index for the ImageRegion.

IntensityWindowingImage

• Usage: IntensityWindowingImage inputImage minValue maxValue windowMinValue windowMaxValue
• Description: Rescale an image. The windowMinValue and windowMaxValue are remapped to minValue and maxValue in the resulting image. Values below this interval are mapped to a constant. Values over the interval are mapped to another constant.
• NOTE: We should support an alternate output data-type

LargestRegionFilledMask

• Usage: LargestRegionFilledMask GivenImage LowerThresh UpperThresh ClosingSize
• NOTE: Determine if this script is still needed.

LoadImage

• Usage: LoadImage ImageFileName DataType
• Description: Load the image specified in ImageFileName using the data-type specified by the user. See CastImage for a list of valid data-types.

MaskImage

• Usage: MaskImage inputImage inputMask ?outsideValue?
• Description: Clip an image using the specified mask image. The default replacement voxels outside the mask is specified by the optional outsideValue which defaults to 0.

measureVolumeLabelImage

• Usage: measureVolumeLabelImage inputImage
• Description:Measure the volume of each label in the label map. GET Result FORMAT

measureLabelImageStatistics

• Usage: measureLabelImageStatistics labelMap inputImage
• Description:

• measureImageStatistics { inputImage } {

MedianImageFilter

• Usage: MedianImageFilter inputImage ?size?
• Description: Median filter an image using the specified structuring element size. The default size is 1,1,1. Size is a list of size three to define the size in each dimension.
• Note: The size list is specifying the size in voxels and not image units.

NotImage

• Usage: NotImage inputImage
• Description: Compute the logical NOT of an image. It is expected that the image is binary and that this will invert the image.

NotImage

• Usage: OrImage inputImage1 inputImage2
• Description: Compute the logical OR between two images.

• RegionOfInterestImage {inputImage roi }

NotImage

• Usage: RelabelComponentImage inputImage ?minimumSize?
• Description: Relabel an label map image. The labels are put into descending order based on the size. Therefore image label 1 is the label with the largest size. The minimum label size can be specified by the user by specifying the minimumSize argument. By default the minimumSize is 0. This size is specified in image units (typically mm3).

ResampleImage

• ResampleImage {inputImage transform outputDataType {interpolatorType Linear} {resolution {1.0 1.0 1.0}} {dimensions {256 256 256}} {origin {0.0 0.0 0.0}} }

ResampleImageWithReferenceImage

• ResampleImageWithReferenceImage {inputImage transform referenceImage {interpolatorType Linear} {RequestedDataType "Signed-16bit"} {DefaultPixelValue 0} }

RescaleImage

• RescaleImage {inputImage outputDataType {minValue 0} {maxValue 255} }

SaveImage

• Usage: SaveImage inputImage ImageFileName
• Description: Save the specified image to the provided file name. The file name extension is used to determine the file type.
• File Format Extensions:
  • NifTI: .nii, .nii.gz
  • Meta: .mhd, .mha
  • NRRD: .nhdr

ShiftScaleImage

• Usage: ShiftScaleImage inputImage shift scale
• Description: Shift and scale the image intensity as specified by the shift and scale values. *Note: Currently the output data type must match the input.

SignedDistanceImage

• Usage: SignedDistanceImage inputImage
• Description: Generate a signed distance floating point image from a binary image or label map. The image is first cast to Unsigned-8bit data and then a Maurer distance image is created where inside the region is positive and outside is negative.
• NOTE: Add support for Danielsson distance

JointCommonMaskEstimationFromSTAPLEFilter

• JointCommonMaskEstimationFromSTAPLEFilter {MaskFileNameList OutputImageFile}

ThresholdImage

• Usage: ThresholdImage inputImage minValue maxValue ?outsideValue?
• Description: Threshold an image between the provided minimum and maximum values. The grey scale values between these two values (inclusive) retain their current greyscale values. Values out side this range are set to the outsideValue which defaults to zero.

BinaryThresholdImage

• Usage: BinaryThresholdImage inputImage lowerThreshold upperThreshold ?invertFlag? ?OutputDataType?
• Description: Threshold an image between the provided minimum and maximum values. The grey scale values between these two values (inclusive) are set to 1, and values outside this range are set to 0. This can be inverted to perform a logical NOT on the binary image at the time that the thresholding is performed.

Brains::itkUtils namespace

convertBrainsDataTypeStringToItk

• Usage: convertBrainsDataTypeStringToItk brainsDataType
• Description: Returns the Wrap ITK pixel type specified by the string. If the string specifies another pixel type, Unsupported is returned.

getItkImageType

• Usage: getItkImageType image
• Description: Returns the ITK image type specified by the string. If the string specifies another pixel type, Unsupported is returned.

GetImageMin

• Usage: GetImageMin image
• Description: Returns the image minimum pixel value.

GetImageMax

• Usage: GetImageMax image
• Description: Returns the image maximum pixel value.

GetItkImageSize

• Usage: GetItkImageSize image
• Description: Returns the image size in a list.

GetItkImageSpacing

• Usage: GetItkImageSpacing image
• Description: Returns the image spacing in a list.

GetItkImageOrigin

• Usage: GetItkImageOrigin image
• Description: Returns the image origin in a list.

readItkTransform

• Usage: readItkTransform filename
• Description: Return the Transform provided in the user specified file. Currently this can load any ITK transform that supports the TransformIO mechanism. That is they support the Get/Set Paramaters and FixedParameters. This currently excludes: IdentityTransform, Rigid3DPerspectiveTransform, and ScaleTransform. Support is only included for transform with parameters of type double and with three dimensions.

WriteItkTransform

• Usage: WriteItkTransform transform transformFileName
• Description: Write the specified transform to a file

Brains::External Namespace

runConvertImageType

• Usage: runConvertImageType InputImage OutputImage ?DataType?
• Description: Convert from DICOM format to a standard format as specified by the image filename extension. The DataType can be one of the following
  • Unsigned char - 1
  • Signed Short - 2
  • Float - 3

runClipInferior

• Usage: runClipInferior InputImage OutputImage ?DistanceBelowOrigin?
• Description: This procedure will run BRAINSClipInferior to clip the inputVolume and write the resulting clipped image to the specified file. The default DistanceBelowOrigin is 80.0mm.

runACPCDetect

• Usage: runACPCDetect InputImage ACPCModel OutputDir OutputImage OutputTransform OriginalLandmarks OutputLandmarks ?rescaleIntensities? ?UseWindowedSinc?
• Description: Run BRAINSConstellationDetector to put the image into AC-PC alignment. By default the program will rescale image intensities, and not use linear interpolation. To turn off rescaleIntensities set its value to zero, and to enable UseWindowedSinc set this to as positive integer value.

runRigidRegistration

• Usage: runRigidRegistration MovingImage FixedImage OutputTransform ?samples? ?translationScale? ?iterations? ?minimumStepSize? ?InitialTransform? ?failureExitCode? ?OutputImage? ?PixelType? ?UseWindowedSinc? ?InitializeMode? ?MaskMode?
• Description: Run rigid version of BRAINSFit. NOTE: This procedure is deprecated and will be merged with runBRAINSfit

runClipROIAUTO

• Usage: runClipROIAUTO InputImage OutputClippedImage ?OutputImagePixelType?
• Description: Run BRAINSROIAuto to produce a clipped image. NOTE: Merge with runMaskROIAUTO

runMaskROIAUTO

• Usage: runClipROIAUTO InputImage OutputMaskImage ?closingSize? ?otsuPercentileThreshold? ?thresholdCorrectionFactor?
• Description: Run BRAINSROIAuto to produce a clipped brain image. NOTE: Merge with runClipROIAUTO

runBRAINSFit

• Usage: runBRAINSFit MovingImage FixedImage ?TransformType? ?OutputTransform? ?Samples? ?TranslationScale? ?Iterations? ?MinimumStepSize? ?InitialTransform? ?FailureExitCode? ?OutputImage? ?PixelType? ?UseWindowedSinc? ?FixedTimeIndex? ?MovingTimeIndex? ?InitializeMode? ?MaskMode? ?ReproportionScale? ?SkewScale? ?SplineGridSize? ?NumberOfHistogramBins? ?NumberOfMatchPoints? ?HistogramMatch? ?PermitParameterVariation?
• Description: Run BRAINSFit supporting modifying all exposed command line parameters

runBrainsMush

• Usage: runBrainsMush T1Image T2Image MushImage BrainMask ?InputMask? ?BoxStartX? ?BoxStartY? ?BoxStartZ? ?BoxSizeX? ?BoxSizeY? ?BoxSizeZ?
• Description: Run BRAINSMush to generate a brain mask by adding together the T1 and T2 weighted images. The initial search region is defined either by a mask region of a bounding box specified in voxels.

runKmeansClassification

• Usage: runKmeansClassification T1Image BrainMask KMeansLabelMap ?LabelThresholdValue? ?ClipArterialBlood?
• Description: Run BRAINSKmeansClusterSamples to perform a K-Means classification of a T1 weighted image.

runRandomSampleClassPlugs

• Usage: runRandomSampleClassPlugs KmeansLabelMap OutputPlugImage ?NumberOfPlugs? ?PlugScarcity?
• Description: Run BRAINSRandomSampleClassPlugs to randomly sample a label map. The use specifies the number of plugs and the plug scarcity to determine the number of plugs to sample.

runRandomSampleClassPlugs

• Usage: runBRAINSClassPlugs T1AcpcImage T2AcpcImage PDAcpcImage BrainMask GreyPlugs WhitePlugs CsfPlugs VbPlugs ?plugClassNames? ?t1ClassMeans? ?t2ClassMeans? ?pdClassMeans? ?randomSeed? ?numberOfPlugs? ?coverage? ?permissiveness? ?meanOutlier? ?varOutlier? ?plugSize? ?partitions? ?numberOfClassPlugs? ?bloodMode? ?bloodImage?
• Description: Run BRAINSClassPlugs to define exemplars for the BRAINS tissue classification code. The default class means are given the following values (order is GM, MW, CSF, Venous Blood)
  • T1 Class Means: 80.186111, 113.979065, 30.087282, 10.8
  • T2 Class Means: 117.773056, 84.270554, 222.857208, 68.8
  • PD Class Means: 173.143585, 140.521729, 190.218933, 47.0

runBRAINSClassify

• Usage: runBRAINSClassify T1AcpcImage T2AcpcImage PDAcpcImage BrainMask GreyPlugs WhitePlugs CsfPlugs VbPlugs classVolume ?grossTrim? ?spatialTrim? ?spatialX? ?spatialY? ?spatialZ? ?spatialXX? ?spatialYY? ?spatialZZ? ?spatialXY? ?spatialXZ? ?spatialYZ? ?histogramEqualize? ?generateSeperateImages? ?excludeVolume?
• Description: Run BRAINS tissue classification algorithm.

runBRAINSDiscreteClass

• Usage: runBRAINSDiscreteClass ClassImage DiscreteImage ?BasalMask? ?BasalThreshold?
• Description: Run BRAINSDiscreteClass - Convert a BRAINS continuous tissue classification into a discrete classification

runN4ITK

• Usage: runN4ITK InputVolume OutputVolume ?BiasVolume? ?MaskVolume? ?ShrinkFactor?
• Description: Run N4ITK - Bias field correction

runBayesianClassification

• Usage: runBayesianClassification T1Image T2Image PDImage PlugLabelMap KMeansLabelMap BayesianLabelMap ClassStatsFile
• Description: Run BayesianClassifier - Bayesian tissue classifier (discrete)

runBiasCorrector

• Usage: runBiasCorrector InputImage BrainMask ClassMeans ClassSigma OutputImage ?Degree?
• Description: Run BiasCorrector - Styner Bias field correction algorithm

runCreateTalairachParameters

• Usage: runCreateTalairachParameters InputImage AC PC SLA IRP TalairachBoxFile TalairachGridFile
• Description: Run BRAINSTalairach to define the Talairach Bounding box and grid

runCreateTalairachMask

• Usage: runCreateTalairachMask InputImage TalairachGridFile TalairachBox OutputMask ?Mode? ?Expand?
• Description: Run BRAINSTalairachMask to define a mask based on the Talairach atlas

runBRAINSDemonsWarp

• Usage: runBRAINSDemonsWarp MovingImage FixedImage DeformationField OutputImage ?HistogramBins? ?MatchPoints? ?PyramidLevels 5} ?LevelIterations? ?FilterSize? ?InputPixelType? ?OutputPixelType? ?RegistrationType? ?DeformationFieldSigma? ?InitialTransform?
• Description: Run BRAINSDemonWarp - Nonlinear image registration

runApplyWarp

• Usage: runApplyWarp MovingImage FixedImage TransformType TransformFile OutputImage ?DataType? ?InterplotationType? ?defaultValue?
• Description: Run BRAINSResample - Resample an image based on a deformation field or ITK transform

runFullBRAINSABC

• Usage: runFullBRAINSABC T1ImageList T2ImageList AtlasDir BRAINSABC_resultNames maxIterations Tolerance BiasFieldDegree OutputDir ?UseWindowedSinc?
• Description: Run full BRAINSABC algorithm including registration

runSimpleEM

• Usage: runSimpleEM T1Image T2Image TemplateImage AtlasImageList ?Iterations? ?Tolerance? ?BiasFieldDegree? ?PriorWeightList?
• Description: Run simpleEM - BRAINSABC Segmentation/Classification from UNC

runBrainsCortex

• Usage: runBrainsCortex ImageFile OutputSurface ?SurfaceValue? ?DepthValue? ?HighValue? ?ContourValue? ?MaxRMSError? ?TargetReduction? ?NumIterations? ?PassBand? ?MaxDepth? ?AntiAliasFlag? ?MeasureDepth? ?MeasureCurvature? ?PreserveTopology? ?BoundarySmoothing? ?FeatureEdgeSmoothing? ?NormalizeCoordinates? ?KeepLargestConnected?
• Description: Create the brain surface to estimate both curvature and cortical depth

runBRAINSApplySurfaceLabels

• Usage: runBRAINSApplySurfaceLabels labelMapFile inputSurfaceFile outputLabelName outputSurfaceFile
• Description: Label a surface using a label map. Each cell is assigned a label from the map, or zero if no label intersects the cell.

runBRAINSMeasureSurface

• Usage: runBRAINSMeasureSurface surfaceFile scalarArrayName labelNameList outputCsvFile ?subjectId? ?scanId? ?outputXmlFile?
• Description: Label a surface using a label map. Each cell is assigned a label from the map, or zero if no label intersects the cell.