Command Line Applications

(Note: This page is automatically generated. Please do not attempt to edit it!)

NifTK also contains a large array of command line Applications. These are briefly listed in the table below. The left column links to a page describing the command line usage, and the right column is the first two lines from the usage message.

Known Caveats

• Please read some background on file I/O in NifTK.
• Most file read/write is based on file extensions, with each file reader/writer being implemented by different classes and hence different authors in ITK/MITK/NifTK. Thus users should be aware that there may be different behaviour for different file types. The only way to be sure is to test each application for your own file type of interest.
• Many ITK filters work on a voxel by voxel basis, such as adding, subtracting and multiplying images. By this we mean that image geometry such as origin, spacing, orientation etc. are not checked.

niftk2DImagesTo3DVolume	Program to compose a 3D volume from individual 2D images.
niftkAbsImageFilter	Runs the ITK AbsImageFilter on a single image to output the absolute value image, useful for displaying the image properly in MIDAS
niftkAdd	USAGE: niftkAdd [–returnparameterfile <std::string>]
niftkAddBorderToImage	USAGE: niftkAddBorderToImage [–returnparameterfile <std::string>]
niftkAffine	USAGE: niftkAffine [–returnparameterfile <std::string>]
niftkAnd	Runs the ITK AndImageFilter to add two images of equal sizes on a voxel by voxel basis.
niftkAnonymiseDICOMImages	USAGE: niftkAnonymiseDICOMImages [–returnparameterfile <std::string>]
niftkAnonymiseDICOMMammograms	USAGE: niftkAnonymiseDICOMMammograms [–returnparameterfile <std::string>]
niftkApplyMaskToImage	USAGE: niftkApplyMaskToImage [–returnparameterfile <std::string>]
niftkAtlasStatistics	Takes an atlas, containing a set of image labels, and for each input image,
niftkAtrophyCalculator.py	This script is for atrophy calculation using Boundary Shift Integral (BSI).
niftkAverage	Uses ITK ImageFileReader to load any number of input images, creating the arithmetic mean on a voxel by voxel basis, writing the output with ITK ImageFileWriter. All input images must be the same size, and are converted to float on input, and hence are float on output.
niftkAverageStationaryChessboards	Takes a two directories of images, extracts chessboards,
niftkAverageTrackingMatrices	Takes a directory, tries to load all files as 4x4 tracking
niftkBackProject2Dto3D	Back projects a 2D image into a 3D volume
niftkBasicImageFeatures	Program to compute basic image features for a 2D image.
niftkBasicImageFeatures3D	Program to compute basic image features for a 3D image.
niftkBETter.py	Traceback (most recent call last): File "/scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/niftkBETter.py", line 367, in <module>
niftkBiasFieldCorrection.py	This script is for N3 or N4 bias field correction using Boyes et al. Neuroimage 2008 normalization process.
niftkBifurcationToPointSet	Takes VTK PolyLines and converts to MITK
niftkBilateralImageFilter	Bilteral filter from ITK. See itk::BilateralImageFilter.
niftkBinaryShapeBasedSuperSamplingFilter	Program to super-sample a mask in a specific dimension via shape based interpolation.
niftkBlockMatching	Implements Block Matching, based on Ourselin et. al., Image and Vision Computing, 19 (2000) 25-31 and Includes modifications from Ourselin et. al. MICCAI 2002 pp 140-147.
niftkBreastDCEandADC	USAGE: niftkBreastDCEandADC [–returnparameterfile <std::string>]
niftkBreastDensityCalculationGivenMRISegmentation	USAGE: niftkBreastDensityCalculationGivenMRISegmentation
niftkBreastDensityFromMRIs	USAGE: niftkBreastDensityFromMRIs [–returnparameterfile <std::string>]
niftkBreastDensityFromMRIsGivenMaskAndImage	USAGE: niftkBreastDensityFromMRIsGivenMaskAndImage [–returnparameterfile
niftkBreastDicomSeriesReadImageWrite	Program to convert the content of a DICOM directory into breast image volumes.
niftkBreastMaskSegmentationFromMRI	Program to segment left and right breasts from a 3D MR volume.
niftkBSI	Classic BSI. Program to calculate the boundary shift integral, based on the paper: Freeborough PA and Fox NC, The boundary shift integral: an accurate and robust measure of cerebral volume changes from registered repeat MRI, IEEE Trans Med Imaging. 1997 Oct;16(5):623-9.
niftkCameraCalibration	Calibrates a video camera from a directory containing
niftkCombineSegmentations	Merges several segmentations together to create a single best segmentation using
niftkCommonUnitTests	Available tests: 0. niftkConversionUtilsTest
niftkComposeITKAffineTransformations	Compose a pair of affine transformations (see also: niftkMultiplyTransformation).
niftkComputeImageHistogram	Program to calculate the histogram of an image.
niftkComputeJointHistogram	Program to generate a 2D histogram image from a pair of input images. The input images must have the same dimensions.
niftkComputeMeanTransformation	Compute the geometric mean of the transformation.
niftkConnectedComponents	Runs ITK ConnectedComponentImageFilter to find connected components.
niftkConvertImage	USAGE: niftkConvertImage [–returnparameterfile <std::string>]
niftkConvertImageToDICOM	USAGE: niftkConvertImageToDICOM [–returnparameterfile <std::string>]
niftkConvertImageToVTKStructuredGrid	Transform's an image, as read by ITK, into a VTK structured grid. This program was written because ITK only writes VTK structured points, which doesn't include direction cosines.
niftkConvertMidasStrToNii	Convert a Jacobian file in MIDAS str format to nii format.
niftkConvertNiftiVectorImage	Converts a 3D nifti vector valued image into another format.
niftkConvertPLYtoVTK	Program to convert a Stanford University PLY polygonal file format and convert it to VTK format.
niftkConvertRawDICOMMammogramsToPresentation	USAGE: niftkConvertRawDICOMMammogramsToPresentation [–returnparameterfile
niftkConvertToMidasStr	Output a Jacobian file in MIDAS str format.
niftkConvertTransformToRIREFormat	Converts an ITK transformation file to that required by Vanderbilt's Retrospective Image Registration Evaluation project.
niftkCorrectVideoDistortion	Distortion corrects a video (.avi) or image (.jpg, .png)
niftkCreateAffineTransform	Creates an ITK affine transformation from user specified parameters.
niftkCreateAffineTransform2D	Creates an ITK 2D affine transformation from user specified parameters.
niftkCreateMaskFromLabels	Given an image and a list of labels, will output a binary mask, where all voxels with
niftkCreateMaskImage	USAGE: niftkCreateMaskImage [–returnparameterfile <std::string>]
niftkCreateTransformation	Program to create a transformation from a user specified list of parameters.
niftkCropImage	USAGE: niftkCropImage [–returnparameterfile <std::string>]
niftkCTEAcosta2009Subsampling	Implements the subsampling described in section 3.2 and 3.2.1 of Acosta et. al. MIA 13 (2009) 730-743 doi:10.1016/j.media.2009.07.03
niftkCTEAssignAtlasValues	Takes an atlas, and an input image, and for each voxel in the input image that is not background
niftkCTEBourgeat2008	Implements Bourgeat et. al. ISBI 2008,
niftkCTEDas2009	Implements "Registration based cortical thickness measurement" S. R. Das et. al., NeuroImage 45 (2009) 867-879
niftkCTEExtractGMWMBoundaryFromLabelImage	From a given label image, assumed to have 3 values, one for GM, one for WM and one for CSF, will extract the GM/WM boundary.
niftkCTEHighRes	Implements a high resolution version of Bourgeat et. al. ISBI 2008, to calculate cortical thickness
niftkCTEHuttonLayering	Implements Chloe Hutton's method for detecting sulcal CSF via adding layers of GM and iteratively calculating thickness
niftkCTEJones2000	Implements Jones et. al. Human Brain Mapping 11:12-32(2000), with optional Gauss-Seidel optimisation,
niftkCTEMaskedSmoothing	Takes a data image (eg. thickness) and a binary mask, and for each voxel in the mask image > 0
niftkCTEPrepareVolumes	Takes up to 5 volumes, each one being a probability map with values [0-1],
niftkCTEYezzi2003	Implements Yezzi and Prince, IEEE TMI Vol. 22, No. 10, Oct 2003,
niftkCurveFitRegistration	Program to register a temporal image sequence using a B-Spline smoothness contraint in the time access.
niftkDecimatePolyData	Runs the VTK vtkDecimatePro filter on a vtkPolyData.
niftkDecomposeAffineMatrix	Decomposes an affine transformation.
niftkDeformationFieldTargetRegistrationError	Calculates the error between two deformation fields which act in the same direction. Error calculated at voxel positions of mask or deformation field 1.
niftkDenoise	USAGE: niftkDenoise [–returnparameterfile <std::string>]
niftkDicomSeriesReadImageWrite	Program to convert the content of a DICOM directory into image volumes.
niftkDilate	USAGE: niftkDilate [–returnparameterfile <std::string>]
niftkDilateMaskAndCrop	Runs Fluid Cropping process
niftkDistanceTransform	Runs the ITK DanielssonDistanceMapImageFilter, specifically for binary images, outputting the distance transform.
niftkDoubleWindowBSI	Program to calculate the double window boundary shift integral, based on the paper Freeborough PA and Fox NC, The boundary shift integral: an accurate and
niftkDynamicContrastEnhancementAnalysis	Program to analyse a set of dynamic contrast enhancement images.
niftkElasticBodySplineWarp	USAGE: niftkElasticBodySplineWarp [–returnparameterfile <std::string>]
niftkErode	USAGE: niftkErode [–returnparameterfile <std::string>]
niftkEvaluateIntrinsicParametersOnNumberOfFrames	Interogates a tracking and video directory for tracking
niftkEVFFCECT	USAGE: niftkEVFFCECT [–returnparameterfile <std::string>]
niftkExportDICOMTagsToCSVFile	USAGE: niftkExportDICOMTagsToCSVFile [–returnparameterfile <std::string>]
niftkExtract2DSliceFrom3DImage	USAGE: niftkExtract2DSliceFrom3DImage [–returnparameterfile <std::string>]
niftkExtractCurvatures	Computes Gaussian, mean, minimum or maximum curvatures of a scalar image.
niftkExtractRegion	Runs ITK ExtractRegion image function
niftkExtractScalp	Implements Dogdas et al. Human Brain Mapping 26:273-285(2005) to extract the scalp.
niftkExtractZeroCrossing	Runs ITK ZeroCrossingImageFilter.
niftkExtrudeMaskToVolume	USAGE: niftkExtrudeMaskToVolume [–returnparameterfile <std::string>]
niftkFileUnitTests	Available tests: 0. niftkFileHelperTest
niftkFillHoles	Fill hols in an image using itk::VotingBinaryIterativeHoleFillingImageFilter.
niftkFindAndTriangulateCrossHair	Interogates a tracking and video directory for tracking
niftkForwardAndBackProjectionDifferenceFilter	Compute the difference between a set of projection images and a reconstruction estimate (or zero).
niftkForwardProject3Dto2D	Projects a 3D image volume into 2D
niftkGaussian	Runs the ITK DiscreteGaussianImageFilter.
niftkGetMatchedTrackingMatrix	Interogates a tracking and video directory for tracking
niftkGetMetricValue	This program returns a metric value between two input files
niftkGetTrackerStats	Read a framemap log file and tracking directories and get
niftkGradientVectorField	Take the gradient of an image, and outputs a vector image. Mainly used for generating test images.
niftkHandeyeCalibration	Determines the hand eye calibration for a tracked object,
niftkHandeyeCalibrationFromDirectory	Interogates a tracking and video directory for tracking
niftkHandeyeCalibrationUsingRegistration	Determines the hand eye calibration for a tracked object,
niftkHistogramEqualization	USAGE: niftkHistogramEqualization [–returnparameterfile <std::string>]
niftkHistogramMatchingImageFilter	USAGE: niftkHistogramMatchingImageFilter [–returnparameterfile <std::string>]
niftkIGIMakeGeometry	"backwall") Make geometry for visualisation of laparoscopic tracking
niftkImageFeatureMatching	Runs stereo matching with a Seqpential CPU
niftkImageInfo	Prints image hader information.
niftkImageMomentsRegistration	USAGE: niftkImageMomentsRegistration [–returnparameterfile <std::string>]
niftkImageReconstruction	Compute a reconstructed volume from a set of projection images and an initial estimate (or zero).
niftkInject	Injects a mask image into the input image
niftkInvertAffineTransform	Inverts an affine transform
niftkInvertImage	USAGE: niftkInvertImage [–returnparameterfile <std::string>]
niftkInvertTransformation	Inverts an affine transform
niftkIterativeClosestPointRegister	Runs ICP on a target and source object
niftkITKAffineResampleImage	Transform an image using an ITK affine transformation (see also: niftkTransformation).
niftkJacobianStatistics	Takes a jacobian image and a mask and calculates statistics for the masked region
niftkKmeansClassifier
niftkKMeansWindowBSI	K-BSI: Program to calculate the boundary shift integral, based on the paper Freeborough PA and Fox NC, The boundary shift integral: an accurate and
niftkKMeansWindowWithLinearRegressionNormalisationBSI	Program to calculate the boundary shift integral, based on the paper Freeborough PA and Fox NC, The boundary shift integral: an accurate and
niftkKNDoubleWindowBSI	Program to calculate the k-means normalised double window boundary shift integral, based on the paper Freeborough PA and Fox NC, The boundary shift integral: an accurate and
niftkLaparoscopeTrackingAccuracy	Interogates a tracking and video directory for tracking
niftkLinearSubdivisionPolyDataFilter	Runs the VTK vtkLinearSubdivision filter on a vtkPolyData.
niftkLogInvertImage	USAGE: niftkLogInvertImage [–returnparameterfile <std::string>]
niftkMakeChessBoardPointSet	Generates an MITK Chessboard (Grid) PointSet from 3
niftkMakeGridOf2DImages	Takes filename prefix and suffix, searches for matching
niftkMakeLapUSProbeAprilTagsModel	Generates a VTK model to match the April Tags board created
niftkMakeLapUSProbeAprilTagsVisualisation	USAGE: niftkMakeLapUSProbeAprilTagsVisualisation [–returnparameterfile
niftkMakeLapUSProbeARUCOModel	USAGE: niftkMakeLapUSProbeARUCOModel [–returnparameterfile <std::string>]
niftkMakeLapUSProbeSimulationData	Generates Test Data for simulating probe
niftkMakeMaskImagesFromStereoVideo	Interogates a tracking and video directory for tracking
niftkMammogramCharacteristics	Program to compute basic characteristics of a mammogram.
niftkMammogramFatSubtraction	USAGE: niftkMammogramFatSubtraction [–returnparameterfile <std::string>]
niftkMammogramMaskSegmentation	USAGE: niftkMammogramMaskSegmentation [–returnparameterfile <std::string>]
niftkMammogramPectoralisSegmentation	USAGE: niftkMammogramPectoralisSegmentation [–returnparameterfile
niftkMammographicTumourDistribution	USAGE: niftkMammographicTumourDistribution [–returnparameterfile
niftkMapVolumeDataToPolyDataVertices	Takes an image and a VTK PolyData, and for each vertex, interpolates the image, and stores the scalar value with the vertex.
niftkMarchingCubes	Takes an image as a VTK structured grid (NOT structured points), and performs a marching cubes iso-surface extraction.
niftkMaskDICOMMammograms	USAGE: niftkMaskDICOMMammograms [–returnparameterfile <std::string>]
niftkMergePointClouds	Merges separate point clouds into one.
niftkMTPDbc	Perform the differential bias correction on the two images.
niftkMTPFillLesions.py	This script is for multi-modality and multi-time-point lesion filling using the patch-based method Prados et al. MICCAI 2014.
niftkMultiply	USAGE: niftkMultiply [–returnparameterfile <std::string>]
niftkMultiplyTransformation	Multiply the two input transformations.
niftkMultiScaleHessianImageEnhancement2D	Program to enhance 2D structures using Hessian eigensystem-based measures in a multiscale framework.
niftkMultiScaleHessianImageEnhancement3D	Program to enhance 3D structures using Hessian eigensystem-based measures in a multiscale framework.
niftkN4BiasFieldCorrection	USAGE: niftkN4BiasFieldCorrection [–returnparameterfile <std::string>]
niftkNegateImage	USAGE: niftkNegateImage [–returnparameterfile <std::string>]
niftkOCTVolumeConstructor	Converts a set of 2D OCT tif files into a 3D volume.
niftkOtsuThresholdImage	USAGE: niftkOtsuThresholdImage [–returnparameterfile <std::string>]
niftkPadImage	Program to enlarge the image size and pad it with a background value. niftkPadImage input output size_x size_y size_z pad_value
niftkPickPointsOnStereoVideo	Interogates a tracking and video directory for tracking
niftkPivotCalibration	Calibrates a Pointer Device using a single point, pivot
niftkPointSetRegister	Registers two point sets, either ordered or using
niftkPointSetStatistics	Reads an MITK point set and outputs some
niftkPointSetTransform	Transforms a point set using a matrix
niftkPrintDICOMSeries	USAGE: niftkPrintDICOMSeries [–returnparameterfile <std::string>]
niftkProject3DPointsToStereoPair	Given a stereo pair of calibrated video images, will take a
niftkProjectionGeometry	Create a set of tomosynthesis projection matrices.
niftkProjectTrackedPointsOnStereoVideo	Interogates a tracking and video directory for tracking
niftkRegionalMammographicDensity	USAGE: niftkRegionalMammographicDensity [–returnparameterfile <std::string>]
niftkRegMNI-T1-B0.py	This script is for MS registration preprocessing. It calculates the transformation from Atlas to T1, and form T1 to B0 following the guidelines of: Muhlert et al. JMRI 2013. DOI: 10.1002/jmri.23970
niftkReorientateImage	This program reorientates, that is flips and/or permutes the voxels of, an image. It can be used to (a) correct the orientation of an image by changing
niftkRescale	Runs ITK RescaleIntensityImageFilter.
niftkRescaleImageUsingHistogramPercentiles	USAGE: niftkRescaleImageUsingHistogramPercentiles [–returnparameterfile
niftkResetDirectionField	Takes a copy of an input image, copying data into another image, where the origin, spacing and direction can be over-written.
niftkResetVoxelDimensionsField	Loads an image in, and sets the voxel size to the ones you specified.
niftkReviewVideoData	Interogates a tracking and video directory for tracking
niftkSampleImage	Program to sub (>1) or super (<1) sample an image, applying appropriate smoothing if required.
niftkScalarConnectedComponentImageFilter	USAGE: niftkScalarConnectedComponentImageFilter [–returnparameterfile
niftkSegmentationStatistics	Computes segmentation statistics between different segmentations. Initially based on Shattuck et. al. NeuroImage 45(2009) 431-439.
niftkSegmentForegroundFromBackground	USAGE: niftkSegmentForegroundFromBackground [–returnparameterfile
niftkSeriesReadVolumeWrite	Program to convert a set of images into a an image volume.
niftkSetBorderPixel	Simply sets the border pixel to the specified value.
niftkShiftProb	This program adjusts prob. output from STAPLE
niftkShiftScale	Runs the ITK ShiftScaleImageFilter.
niftkShrinkImage	Runs the ITK ShrinkImageFilter.
niftkSmoothPolyData	Runs the VTK vtkSmoothPolyDataFilter on a vtkPolyData.
niftkSplitVideo	Looks for a suitably named video and framemap.log file and
niftkSplitVolumeIntoVoxelPlanes	Program to split an image volume into individual planes of voxels.
niftkSTAPLE	This program perform STAPLE on input segmentations.
niftkSubsampleImage	USAGE: niftkSubsampleImage [–returnparameterfile <std::string>]
niftkSubtract	USAGE: niftkSubtract [–returnparameterfile <std::string>]
niftkSubtractSliceFromVolume	Subtracts a 2D image from a specific 3D volume slice.
niftkSwapIntensity	Takes an image and swaps one intensity for another.
niftkT1PDT2Lesions.py	This script fills lesions in the T1 image allowing different ways using the patch-based method Prados et al. MICCAI 2014.
niftkTestCompareImage	Checks scalar images. Will throw exceptions if check fails. By default does nothing. You have to specify at least one test to perform.
niftkTestImage	Generates a 3D test image, either a binary cuboid, binary ellipsoid, grid, or test card type pattern.
niftkThinPlateSplineScatteredDataPointSetToImage	USAGE: niftkThinPlateSplineScatteredDataPointSetToImage [–returnparameterfile
niftkThinPlateSplineWarp	USAGE: niftkThinPlateSplineWarp [–returnparameterfile <std::string>]
niftkThreshold	Runs the ITK BinaryThresholdImageFilter.
niftkTransformation	Transforms an image by a transformation.
niftkTransformPoint3Dto2D	Program to load a 2D-3D transformation and transform a 3D point into 2D.
niftkTransformPolyData	Transform's a VTK Poly Data file by any number of affine transformations.
niftkTriangulate2DPointPairsTo3D	Takes a file of 2D point pairs (left and right), and
niftkTwoTrackerAnalysis	Interogates a tracking and video directory for tracking
niftkUltrasoundPinCalibration	Calibrates an US probe using a single pin/cross-wire
niftkUltrasoundPinCalibrationClicker	Enables the user to scroll through images, and click on a
niftkUltrasoundTransformAndImageMerger	Merges a directory of ultrasound images (*.nii) and
niftkUnaryImageOperatorsOnDirectoryTree	USAGE: niftkUnaryImageOperatorsOnDirectoryTree [–returnparameterfile
niftkVesselExtractor	USAGE: niftkVesselExtractor [–returnparameterfile <std::string>]
niftkVideoHandEyeByCrossCalibration	Calibrates stereo laparoscopic video using a single cross
niftkVideoTestClient	Grabs video via OpenCV and sends via NiftyLink.
niftkVideoToImages	Converts and video file and framemap.log file to a set of
niftkVideoToSurfaces	Interogates a tracking and video directory for tracking
niftkVolToFreeSurfer	Takes a FreeSurfer surface (in ASCII format), and a volume containing (eg.) thickness data, and then for each point in the surface, finds the thickness, either the closest in the neighborhood, or by smoothing and dividing the volume data.
niftkVotingBinaryIterativeHoleFillingImageFilter	USAGE: niftkVotingBinaryIterativeHoleFillingImageFilter [–returnparameterfile
niftkVoxelWiseMaximumIntensities	Uses ITK ImageFileReader to load any number of input images, calculates the maximum intensity on a voxel by voxel basis and writes the output with ITK ImageFileWriter. All input images must be the same size, are converted to float on input, and hence are float on output.
Summary Measure the distance between a set of points and a vtk poly data surface	USAGE: niftkVTKDistanceToSurface [–returnparameterfile <std::string>]
niftkVTKIntegrationTests	Available tests: 0. niftkVTK3PointReaderTest
niftkVTKIterativeClosestPointRegister	USAGE: niftkVTKIterativeClosestPointRegister [–returnparameterfile
niftkVTKUnitTests	Available tests: 0. niftkVTKInterpolateMatrixTest
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