Function reference • ANTsR

All functions
`DesikanKillianyTourville`	DesikanKillianyTourville
`aal`	AAL Labels
`abpBrainExtraction()`	An ants-based brain extraction script.
`abpN4()`	MR image bias correction based on the N4 algorithm.
`addNoiseToImage()`	addNoiseToImage
`affineInitializer()`	a multi-start optimizer for affine registration
`alffmap()`	alffmap
`antsBOLDNetworkAnalysis()`	a basic framework for network analysis that produces graph metrics
`antsMotionCalculation()`	antsMotionCalculation
`antsMotionCorr()`	Motion Correction
`antsSpatialICAfMRI()`	Perform spatial ICA on fMRI bold data.
`antsrMotionCalculation()`	antsrMotionCalculation
`antsrSurf()`	Render a function onto a surface.
`antsrVersions`	antsrVersions
`antsrVol()`	Render an image volume with or without overlay.
`aslAveraging()`	Average ASL tag-control pairs to estimate perfusion
`aslCensoring()`	Censor bad volumes from ASL data.
`aslDenoiseR()`	WIP: data-driven denoising for ASL MRI
`aslPerfusion()`	ASL-based Perfusion from PASL, CASL or pCASL.
`basicInPaint()`	Inpaints missing imaging data from boundary data
`bayesianCBF()`	Uses probabilistic segmentation to constrain pcasl-based cbf computation.
`bayesianlm()`	Simple bayesian regression function.
`blockStimulus()`	Block stimulus model for FMRI Data
`bloodPerfusionSVD()`	Calculate blood perfusion using deconvolution.
`bold_correlation_matrix`	BOLD Correlation Matrix
`clusterTimeSeries()`	Split time series image into k distinct images
`combineNuisancePredictors()`	Combine and reduce dimensionality of nuisance predictors.
`compcor()`	Compcors the input matrix using SVD and returns the result.
`composeTransformsToField()`	Compose arbitrary transform list into a deformation field.
`computeDVARS()`	computeDVARS
`computeDVARSspatialMap()`	computeDVARSspatialMap
`convolveImage()`	convolve one image with another
`corw()`	produces a correlation matrix via weighted correlation.
`createJacobianDeterminantImage()`	createJacobianDeterminantImage
`createWarpedGrid()`	Create a warped grid for visualization.
`crossvalidatedR2()`	Cross-Validated R^2 value
`cvEigenanatomy()`	Cross-validation method for eigenanatomy decompositions.
`deconvolutionSVD()`	Regularize SVD (deconvolution) solution of cerebral blood flow.
`eanatDef()`	Eigenanatomy with deflation
`eanatSelect()`	Selection of n eigenvectors and sparsity for eigenanatomy
`eigSeg()`	Segmentation for eigenanatomy.
`estSmooth()`	Estimate image smoothness
`euler()`	Euler Character
`exemplarInpainting()`	Uses example images to inpaint or approximate an existing image.
`fMRINormalization()`	Multi-run normalization, filtering and nuisance estimation for fMRI.
`fastMarchingExtension()`	Fast Marching Extension filter will extend an intensity or label image from a known region into the unknown region along a geodesic path
`filterfMRIforNetworkAnalysis()`	Basic pre-processing for BOLD or ASL-based network analysis.
`fitBsplineObjectToScatteredData()`	fitBsplineObjectToScatteredData
`frequencyFilterfMRI()`	Band pass filtering for BOLD image.
`fsl2antsrTransform()`	fsl2antsrTransform
`functionalLungSegmentation()`	Ventilation-based segmentation of hyperpolarized gas lung MRI.
`generateAifMaskImage()`	Automatically generate an arterial input function mask.
`geoSeg()`	brain segmentation based on geometric priors
`getASLNoisePredictors()`	Get nuisance predictors from ASL images
`getAverageOfTimeSeries()`	getAverageOfTimeSeries
`getCenterOfMass()`	center of mass
`getMultiResFeatureMatrix()`	build multiple resolution predictor matrix from feature images
`getMultivariateTemplateCoordinates()`	Label multivariate components by an anatomical coordinate system.
`getTemplateCoordinates()`	Define an anatomical coordinate system in a new image based on a template
`getfMRInuisanceVariables()`	Extract generic fMRI nuisance variables for ASL or BOLD
`hemodynamicRF()`	Linear Model for FMRI Data
`histogramMatchImage()`	histogramMatchImage
`icawhiten()`	Simple icawhitening function.
`image2ClusterImages()`	Converts an image to several independent images.
`imageDomainToSpatialMatrix()`	Image domain to spatial position
`initializeEigenanatomy()`	Convert a matrix to a form that can be used to initialize sparse cca and pca.
`initializeSimlr()`	Initialize simlr
`interleaveMatrixWithItself()`	Simple interleaveMatrixWithItself function.
`invariantImageSimilarity()`	similarity metrics between two images as a function of geometry
`jlfProp()`	Propagate Joint Label Fusion (JLF) solutions through a time series
`joinEigenanatomy()`	Simple joinEigenanatomy function.
`jointSmoothMatrixReconstruction()`	joint smooth matrix prediction
`kellyKapowski()`	Compute cortical thickness using the DiReCT algorithm.
`knnSmoothImage()`	k-nearest neighbors constrained image smoothing
`knnSmoothingMatrix()`	k-nearest neighbors constrained smoothing
`labelGeometryMeasures()`	labelGeometryMeasures
`labelImageCentroids()`	labelImageCentroids
`labelOverlapMeasures()`	labelOverlapMeasures
`labels2matrix()`	Convert label image to a matrix
`load.ANTsR()`	Load R sessions with ANTsR objects
`localGyrificationIndex()`	Local gyrification index.
`lowrankRowMatrix()`	Produces a low rank version of the input matrix
`make3ViewPNG()`	Rotate an existing 3d window into different views.
`makeGraph()`	Simple function to create and measure a graph from a square input matrix.
`makePointsImage()`	Create label image from physical space points
`makePowersPointsImage()`	Label image from Powers points
`matrix2timeseries()`	Simple matrix2timeseries function.
`mergeListToNDImage()`	mergeListToNDImage
`mild()`	Efficiently compute a multivariate, image-based (mixed) linear decompositition (mild)
`milr()`	Efficiently compute a multivariate, penalized image-based linear regression model (milr)
`milr.predict()`	Predict from a milr output
`mni2tal()`	Brett's mni2tal
`.motion_correction()`	Simple motion_correction function.
`mrvnrfs()`	multi-res voxelwise neighborhood random forest segmentation learning
`mrvnrfs.predict()`	multi-res voxelwise neighborhood random forest segmentation
`multiLabelMorphology()`	Morphology on multi label images.
`multiResRandomForestRegression()`	multiple resolution neighborhood random forest regression
`multichannelPCA()`	Shape analysis of multichannel images based on PCA
`multichannelToVector()`	Convert multichannel `antsImage` to a vector.
`multiscaleSVD()`	Multi-scale svd
`networkEiganat()`	Convenience wrapper for eigenanatomy decomposition.
`orthogonalizeAndQSparsify()`	sparsify a matrix
`pairwiseImageDistanceMatrix()`	Simple pairwiseImageDistanceMatrix function for images
`partialVolumeCorrection()`	Perform partial volume correction for ASL images.
`perfusionregression()`	Perfusion Regression
`petSUVR()`	Compute SUVR from PET time series images
`plotBasicNetwork()`	Simple plotBasicNetwork function.
`plotPrettyGraph()`	Simple plotPrettyGraph function saves to png.
`powers_areal_mni_itk`	powers_areal_mni_itk
`predictSimlr()`	predict output matrices from simlr solution
`preprocessRestingBOLD()`	Preprocess resting BOLD fMRI image data.
`preprocessfMRI()`	Preprocess BOLD fMRI image data.
`priorBasedSegmentation()`	spatial prior-based image segmentation.
`quantifyCBF()`	quantifyCBF
`quantifySNPs()`	Simple quantifySNPs function.
`randcca()`	randomized cca function.
`randsvd()`	randomized svd function.
`randwhiten()`	randomized whitening function.
`rapidlyInspectImageData()`	Simple rapidlyInspectImageData function.
`readNormalizedPopulationData()`	Read normalized population from h5 file or directory
`reflectImage()`	reflectImage
`reflectionMatrix()`	reflectionMatrix
`regressProjections()`	Regression on image set projection
`regressionNetworkViz()`	Visualize a regression result by a d3 network visualization.
`regularizeSimlr()`	Automatically produce regularization matrices for simlr
`reho()`	REHO
`renderImageLabels()`	3D surface-based rendering of image segmentation labels
`renderSurfaceFunction()`	3D surface-based rendering of volume images.
`renormalizeProbabilityImages()`	Normalize (modified) probability images
`reorientImage()`	reorient image by its principal axis
`resels()`	Estimates image resels
`rfSegmentation()`	A rfSegmentation function.
`rfSegmentationPredict()`	A rfSegmentationPredict function.
`rftPval()`	RFT p-values
`rftResults()`	RFT Statistical Results
`robustMatrixTransform()`	Simple robustMatrixTransform function.
`rsfDenoise()`	WIP: data-driven denoising for resting state fMRI
`save.ANTsR()`	Save R sessions including ANTsR objects
`segmentShapeFromImage()`	convolution-based shape identification
`segmentationRefinement.predict()`	Segmentation refinement using corrective learning (prediction)
`segmentationRefinement.train()`	Segmentation refinement using corrective learning (training)
`simlr()`	Similarity-driven multiview linear reconstruction model (simlr) for N modalities
`simlr2()`	Similarity-driven multiview linear reconstruction model (simlr) for two modalities
`simlrU()`	Compute the low-dimensional u matrix for simlr
`simulateDisplacementField()`	simulateDisplacementField
`skeletonize()`	Skeletonize a binary segmentation.
`smoothAppGradCCA()`	cca via sparse smooth matrix prediction
`smoothMatrixPrediction()`	smooth matrix prediction
`smoothMultiRegression()`	Reconstruct a n by k vector given n by p matrix of predictors.
`smoothRegression()`	smooth matrix-based regression
`sparseDecom()`	Convenience wrapper for eigenanatomy decomposition.
`sparseDecom2()`	Convenience wrapper for 2-view eigenanatomy decomposition.
`sparseDecom2boot()`	Convenience wrapper for 2-view eigenanatomy decomposition w/bootstrap initialization.
`sparseDecomboot()`	Convenience wrapper for eigenanatomy decomposition.
`sparseDistanceMatrix()`	Create sparse distance, covariance or correlation matrix
`sparseDistanceMatrixXY()`	Create sparse distance, covariance or correlation matrix from x, y
`sparseRegression()`	Sparse regression on input images.
`spatialbayesianlm()`	spatially constrained bayesian regression function.
`splitData()`	Split data for testing and training
`splitMask()`	split a mask into n labeled sub-masks
`splitNDImageToList()`	splitNDImageToList
`statFieldThresh()`	Produces a threshold value based on cluster or voxel level statistics
`subgradientL1Regression()`	Simple subgradientL1Regression function.
`subjectDataToGroupDataFrame()`	convert subject matrix data to a row in a dataframe.
`taskFMRI()`	Simple taskFMRI function.
`temporalwhiten()`	Simple autocorrelation-based temporal whitening function.
`testEanat()`	Test eigenanatomy in order
`timeseries2matrix()`	Time-series image to matrix
`timeseriesN3()`	Run N3 on slices of timeseries.
`timeserieswindow2matrix()`	Time-series image to matrix of time windows around user-specified events
`tracts`	tracts
`trapz()`	Calculate the area under a sampled curve (or set of curves).
`vectorToMultichannel()`	Convert vector to multichannel `antsImage`.
`vwnrfs()`	voxelwise neighborhood random forest segmentation and prediction
`vwnrfs.predict()`	voxelwise neighborhood random forest prediction
`weingartenImageCurvature()`	image curvature for 2D or 3D
`whiten()`	Simple whitening function.
`writeNormalizedPopulationData()`	Save normalized population data to a directory or h5 file

Reference

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