Package index • 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.
`pixeltype()` `pixeltype<-`() `components()` `components<-`() `spacing()` `spacing<-`() `direction()` `direction<-`() `origin()` `origin<-`()	Extract Image Attributes `pixeltype` from antsImages
`addNoiseToImage()`	addNoiseToImage
`adjusted_rvcoef()`	Adjusted RV Coefficient
`affineInitializer()`	a multi-start optimizer for affine registration
`alffmap()`	alffmap
`ants.set.seed()`	Set seed for ANTsR functionality
`antsApplyTransforms()`	Apply transforms to images.
`antsApplyTransformsToPoints()`	Apply transforms to points.
`antsAverageImages()`	Computes average of image list
`antsBOLDNetworkAnalysis()`	a basic framework for network analysis that produces graph metrics
`antsCompileFlags()`	return ants compile flags
`antsCopyImageInfo()`	Copy header info
`antsCopyImageInfo2()`	Copy header info with different input order
`antsDir()`	return ANTs binary directory information
`show(<antsImage>)` `initialize(<antsImage>)`	An S4 class for an antsImage
`antsImageClone()`	Clone an `antsImage`.
`antsGetSpacing()` `antsSetSpacing()` `antsGetOrigin()` `antsSetOrigin()` `antsGetDirection()` `antsSetDirection()`	antsImageGetSet
`antsImageHeaderInfo()`	Read file info from image header
`antsImageIterator()`	antsImageIterator
`antsImageIteratorGet()`	antsImageIteratorGet
`antsImageIteratorGetIndex()`	antsImageIteratorGetIndex
`antsImageIteratorGoToBegin()`	antsImageIteratorGoToBegin
`antsImageIteratorGoToReverseBegin()`	antsImageIteratorGoToReverseBegin
`antsImageIteratorIsAtEnd()`	antsImageIteratorIsAtEnd
`antsImageIteratorIsAtReverseEnd()`	antsImageIteratorIsAtReverseEnd
`antsImageIteratorNext()`	antsImageIteratorNext
`antsImageIteratorPrevious()`	antsImageIteratorPrevious
`antsImageIteratorRemaining()`	antsImageIteratorRemaining
`antsImageIteratorSet()`	antsImageIteratorSet
`antsImageIteratorSetIndex()`	antsImageIteratorSetIndex
`show(<antsImageIterator>)` `initialize(<antsImageIterator>)`	An S4 class for an antsImageIterator
`antsImageMutualInformation()`	mutual information between two images
`antsImagePhysicalSpaceConsistency()`	Check for physical space consistency
`antsImageRead()`	Image Read
`Summary(<antsImage>)` `max()` `min()` `range()` `prod()` `sum()` `any()` `all()`	Summary for antsImage Objects
`antsImageTypeCast()`	Cast images to either a passed pixeltype or the most precise of the inputs
`antsImageWrite()`	Image Write
`Math(<antsImage>)` `abs(<antsImage>)` `sign(<antsImage>)` `sqrt(<antsImage>)` `ceiling(<antsImage>)` `round(<antsImage>)` `floor(<antsImage>)` `trunc(<antsImage>)` `log(<antsImage>)` `log10(<antsImage>)` `log2(<antsImage>)` `acos(<antsImage>)` `asin(<antsImage>)` `atan(<antsImage>)` `acosh(<antsImage>)` `asinh(<antsImage>)` `atanh(<antsImage>)` `cos(<antsImage>)` `sin(<antsImage>)` `tan(<antsImage>)` `cosh(<antsImage>)` `sinh(<antsImage>)` `tanh(<antsImage>)` `cospi(<antsImage>)` `sinpi(<antsImage>)` `tanpi(<antsImage>)` `exp(<antsImage>)` `gamma(<antsImage>)` `lgamma(<antsImage>)` `!`(<antsImage>)	Math for antsImage Objects
`Arith(<antsImage>,<antsImage>)` `+`(<antsImage>,<antsImage>) `-`(<antsImage>,<antsImage>) ``(<antsImage>,<antsImage>) `/`(<antsImage>,<antsImage>) `^`(<antsImage>,<antsImage>) `%%`(<antsImage>,<antsImage>) `%/%`(<antsImage>,<antsImage>) `Arith(<antsImage>,<numeric>)` `+`(<antsImage>,<numeric>) `-`(<antsImage>,<numeric>) ``(<antsImage>,<numeric>) `/`(<antsImage>,<numeric>) `^`(<antsImage>,<numeric>) `%%`(<antsImage>,<numeric>) `%/%`(<antsImage>,<numeric>) `+`(<numeric>,<antsImage>) `-`(<numeric>,<antsImage>) `*`(<numeric>,<antsImage>) `/`(<numeric>,<antsImage>) `^`(<numeric>,<antsImage>) `%%`(<numeric>,<antsImage>) `%/%`(<numeric>,<antsImage>) `Arith(<antsImage>,<missing>)` `Arith(<numeric>,<antsImage>)` `Arith(<antsImage>,<logical>)` `Arith(<logical>,<antsImage>)` `Arith(<antsImage>,<array>)` `Arith(<array>,<antsImage>)` `Arith(<list>,<antsImage>)` `Arith(<antsImage>,<list>)` `==`(<antsImage>,<antsImage>) `==`(<antsImage>,<list>) `==`(<antsImage>,<array>) `==`(<array>,<antsImage>) `==`(<antsImage>,<ANY>) `==`(<ANY>,<antsImage>) `>`(<antsImage>,<antsImage>) `>`(<antsImage>,<list>) `>`(<antsImage>,<array>) `>`(<array>,<antsImage>) `>`(<antsImage>,<ANY>) `>`(<ANY>,<antsImage>) `<`(<antsImage>,<antsImage>) `<`(<antsImage>,<list>) `<`(<antsImage>,<array>) `<`(<array>,<antsImage>) `<`(<antsImage>,<ANY>) `<`(<ANY>,<antsImage>) `!=`(<antsImage>,<antsImage>) `!=`(<antsImage>,<list>) `!=`(<antsImage>,<array>) `!=`(<array>,<antsImage>) `!=`(<antsImage>,<ANY>) `!=`(<ANY>,<antsImage>) `<=`(<antsImage>,<antsImage>) `<=`(<antsImage>,<list>) `<=`(<antsImage>,<array>) `<=`(<array>,<antsImage>) `<=`(<antsImage>,<ANY>) `<=`(<ANY>,<antsImage>) `>=`(<antsImage>,<antsImage>) `>=`(<antsImage>,<list>) `>=`(<antsImage>,<array>) `>=`(<array>,<antsImage>) `>=`(<antsImage>,<ANY>) `>=`(<ANY>,<antsImage>) `is.na(<antsImage>)` `anyNA(<antsImage>)` `is.nan(<antsImage>)` `is.infinite(<antsImage>)` `is.finite(<antsImage>)`	Operations for antsImage Objects
`antsIncludes()`	return ANTs installation information
`antsLibs()`	return ants library location
`initialize(<antsMatrix>)`	antsMatrix Class
`antsMotionCalculation()`	antsMotionCalculation
`antsMotionCorr()`	Motion Correction
`antsRegion-class`	An S4 class to hold a region of an antsImage
`antsRegistration()`	Perform registration between two images.
`antsSetPixels()`	Set a pixel value at an index
`antsSpatialICAfMRI()`	Perform spatial ICA on fMRI bold data.
`antsTransformIndexToPhysicalPoint()`	Get Spatial Point from Index
`antsTransformPhysicalPointToIndex()`	Get Index from Spatial Point
`antsVersions`	antsVersions
`antspymm_nuisance_names()`	return nuisance variable strings
`antspymm_predictors()`	Generate Predictors from ANTsPyMM Imaging Data
`antspymm_qc_names()`	Get Quality Control (QC) Metric Names
`antspymm_simlr()`	Perform SiMLR Analysis on Multimodal ANTsPyMM Data
`antspymm_simlr_update_residuals()`	Update Residuals for SiMLR
`antspymm_vartype()`	Determine the Variable Type Based on Its Name
`antsrGetPointerName()`	Return the antsImage pointer string
`show(<antsrMetric>)` `initialize(<antsrMetric>)`	An S4 class for image metrics between two antsImages
`antsrMetricCreate()`	antsrMetricCreate
`antsrMetricGetDerivative()`	antsrMetricGetDerivative
`antsrMetricGetValue()`	antsrMetricGetValue
`antsrMetricInitialize()`	antsrMetricInitialize
`antsrMetricSetFixedImage()`	antsrMetricSetFixedImage
`antsrMetricSetFixedImageMask()`	antsrMetricSetFixedImageMask
`antsrMetricSetFixedTransform()`	antsrMetricSetFixedTransform
`antsrMetricSetMovingImage()`	antsrMetricSetMovingImage
`antsrMetricSetMovingImageMask()`	antsrMetricSetMovingImageMask
`antsrMetricSetMovingTransform()`	antsrMetricSetMovingTransform
`antsrMetricSetNumberOfHistogramBins()`	antsrMetricSetNumberOfHistogramBins
`antsrMetricSetRadius()`	antsrMetricSetRadius
`antsrMetricSetSampling()`	antsrMetricSetSampling
`antsrMotionCalculation()`	antsrMotionCalculation
`antsrSurf()`	Render a function onto a surface.
`show(<antsrTransform>)` `initialize(<antsrTransform>)`	An S4 class for an antsrTransform
`antsrTransformFromDisplacementField()`	antsrTransformFromDisplacementField
`antsrVersions`	antsrVersions
`antsrVol()`	Render an image volume with or without overlay.
`antsrimpute()`	antsrimpute
`apply()`	Extension of apply to allow input of antsImage
`applyAntsrTransform()`	applyAntsrTransform
`applyAntsrTransformToImage()`	applyAntsrTransformToImage
`applyAntsrTransformToPoint()`	applyAntsrTransformToPoint
`applyAntsrTransformToVector()`	applyAntsrTransformToVector
`apply_simlr_matrices()`	Apply simlr matrices to an existing data frame and combine the results
`apply_simlr_matrices_dtfix()`	Apply simlr matrices to an existing data frame and combine the results with DTI naming fix.
`as.antsImage()`	Convert Objects into antsImage objects
`as.antsMatrix()`	Coerce Object to as.antsMatrix
`dim(<antsImage>)` `as.numeric(<antsImage>)` `as.matrix(<antsImage>)` `as.array(<antsImage>)` `as.character(<antsImage>)` `as.factor(<antsImage>)` `factor(<antsImage>)` `as.data.frame(<antsMatrix>)` `as.matrix(<antsMatrix>)` `as.list(<antsMatrix>)`	Coerce antsImage objects to array
`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.
`atropos()`	FMM Segmentation
`ba_svd()`	No fail SVD function that switches to rsvd if svd fails
`basicInPaint()`	Inpaints missing imaging data from boundary data
`bayesianCBF()`	Uses probabilistic segmentation to constrain pcasl-based cbf computation.
`bayesianlm()`	Simple bayesian regression function.
`bigLMStats()`	Efficiently compute basic statistical inference from regressions with multiple outcomes
`blockStimulus()`	Block stimulus model for FMRI Data
`bloodPerfusionSVD()`	Calculate blood perfusion using deconvolution.
`bold_correlation_matrix`	BOLD Correlation Matrix
`boxplot(<antsImage>)`	Boxplot of Values in an Image
`[<-`(<antsImage>,<NULL>,<ANY>,<ANY>) `[<-`(<antsImage>,<logical>,<ANY>,<ANY>) `[<-`(<antsImage>,<array>,<ANY>,<ANY>) `[<-`(<antsImage>,<matrix>,<ANY>,<ANY>) `[<-`(<antsImage>,<list>,<ANY>,<ANY>) `[<-`(<antsImage>,<antsImage>,<ANY>,<ANY>) `[<-`(<antsImage>,<NULL>,<antsRegion>,<ANY>) `[<-`(<antsImage>,<logical>,<antsRegion>,<ANY>) `[<-`(<antsImage>,<array>,<antsRegion>,<ANY>) `[<-`(<antsImage>,<matrix>,<antsRegion>,<ANY>) `[<-`(<antsImage>,<NULL>,<NULL>,<numeric>) `[<-`(<antsImage>,<numeric>,<numeric>,<numeric>) `[<-`(<antsImage>,<numeric>,<NULL>,<numeric>) `[<-`(<antsImage>,<NULL>,<numeric>,<numeric>) `[<-`(<antsImage>,<numeric>,<missing>,<array>) `[<-`(<antsImage>,<missing>,<numeric>,<array>) `[`(<antsImage>,<NULL>,<ANY>,<ANY>) `[`(<antsImage>,<antsImage>,<ANY>,<ANY>) `[`(<ANY>,<antsImage>,<ANY>,<ANY>) `[`(<antsImage>,<logical>,<ANY>,<ANY>) `[`(<antsImage>,<ANY>,<ANY>,<ANY>) `[`(<antsImage>,<NULL>,<NULL>,<ANY>) `[`(<antsImage>,<numeric>,<numeric>,<ANY>) `[`(<antsImage>,<numeric>,<NULL>,<ANY>) `[`(<antsImage>,<NULL>,<numeric>,<ANY>) `[`(<antsImage>,<missing>,<numeric>,<ANY>) `[`(<antsImage>,<numeric>,<missing>,<ANY>) `[`(<antsImage>,<missing>,<missing>,<ANY>)	Extract or Replace Parts of antsImage Object
`buildTemplate()`	ANTs template building.
`check_ants()`	Check if antsImage or read in
`clusterTimeSeries()`	Split time series image into k distinct images
`coerce_mask()`	Simple Mask Maker
`combineNuisancePredictors()`	Combine and reduce dimensionality of nuisance predictors.
`compcor()`	Compcors the input matrix using SVD and returns the result.
`composeAntsrTransforms()`	composeAntsrTransforms
`composeDisplacementFields()`	composeDisplacementFields
`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.
`createAntsrTransform()`	createAntsrTransform
`createJacobianDeterminantImage()`	createJacobianDeterminantImage
`createWarpedGrid()`	Create a warped grid for visualization.
`cropImage()`	crop a sub-image via a mask
`cropIndices()`	crop a sub-image by image indices
`crossvalidatedR2()`	Cross-Validated R^2 value
`cut(<antsImage>)`	Perform Cut on an image
`cvEigenanatomy()`	Cross-validation method for eigenanatomy decompositions.
`deconvolutionSVD()`	Regularize SVD (deconvolution) solution of cerebral blood flow.
`decropImage()`	decrop a sub-image back into the full image
`denoiseImage()`	Denoise an image
`density(<antsImage>)`	Density of Values in an Image
`displacementFieldFromAntsrTransform()`	displacementFieldFromAntsrTransform
`divide_by_column_sum()`	Divide each column by the sum of column absolute values
`eanatDef()`	Eigenanatomy with deflation
`eanatSelect()`	Selection of n eigenvectors and sparsity for eigenanatomy
`eigSeg()`	Segmentation for eigenanatomy.
`error_not_antsImage()`	Stop if not an antsImage object
`estSmooth()`	Estimate image smoothness
`euler()`	Euler Character
`exemplarInpainting()`	Uses example images to inpaint or approximate an existing image.
`exploratory_visualization()`	Exploratory Clustering and Visualization
`extractSlice()`	extract a slice from an 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.
`fitBsplineDisplacementField()`	fitBsplineDisplacementField
`fitBsplineObjectToScatteredData()`	fitBsplineObjectToScatteredData
`fitThinPlateSplineDisplacementField()`	fitThinPlateSplineDisplacementField
`fitTimeVaryingTransformToPointSets()`	fitTimeVaryingTransformToPointSets
`fitTransformToPairedPoints()`	fitTransformToPairedPoints
`frequencyFilterfMRI()`	Band pass filtering for BOLD image.
`fsl2antsrTransform()`	fsl2antsrTransform
`functionalLungSegmentation()`	Ventilation-based segmentation of hyperpolarized gas lung MRI.
`fuzzySpatialCMeansSegmentation()`	fuzzySpatialCMeansSegmentation
`generateAifMaskImage()`	Automatically generate an arterial input function mask.
`geoSeg()`	brain segmentation based on geometric priors
`getANTsRData()`	getANTsRData
`getASLNoisePredictors()`	Get nuisance predictors from ASL images
`getAntsrTransformFixedParameters()`	getAntsrTransformFixedParameters
`getAntsrTransformParameters()`	getAntsrTransformParameters
`getAverageOfTimeSeries()`	getAverageOfTimeSeries
`getCenterOfMass()`	center of mass
`getCentroids()`	Convert an image to the geometric centroids of its signal
`getMask()`	Get Mask
`getMultiResFeatureMatrix()`	build multiple resolution predictor matrix from feature images
`getMultivariateTemplateCoordinates()`	Label multivariate components by an anatomical coordinate system.
`getNeighborhoodAtVoxel()`	Get a hypercube neighborhood at a voxel
`getNeighborhoodInMask()`	Get neighborhoods for voxels within mask
`getPixels()`	Get Pixels
`getTemplateCoordinates()`	Define an anatomical coordinate system in a new image based on a template
`getfMRInuisanceVariables()`	Extract generic fMRI nuisance variables for ASL or BOLD
`glm_impute()`	Impute missing data using GLM models
`gradient_invariant_orthogonality_defect()`	Compute the Gradient of the Orthogonality Defect
`gradient_invariant_orthogonality_salad()`	Gradient of the Invariant Orthogonality Defect Measure
`%>%`	Pipe an object forward
`hausdorffDistance()`	hausdorffDistance
`hemodynamicRF()`	Linear Model for FMRI Data
`hessianObjectness()`	hessianObjectness
`hist(<antsImage>)`	Histogram of Values in an Image
`histogramEqualizeImage()`	histogramEqualizeImage
`histogramMatchImage()`	histogramMatchImage
`histogramMatchImage2()`	Transform image intensities based on histogram mapping.
`iBind()`	iBind
`iMath()`	iMath
`iMathOps`	Operations for iMath Operator
`icawhiten()`	Simple icawhitening function.
`ilr()`	Efficiently compute an image-based linear regression model (ilr)
`ilr.predict()`	Predict from ilr output
`image2ClusterImages()`	Converts an image to several independent images.
`imageDomainToSpatialMatrix()`	Image domain to spatial position
`imageFileNames2ImageList()`	Simple imageFileNames2ImageListing function.
`imageListToMatrix()`	Read Images into a Matrix
`imageSimilarity()`	imageSimilarity
`imagesToMatrix()`	Read Images into a Matrix
`initializeEigenanatomy()`	Convert a matrix to a form that can be used to initialize sparse cca and pca.
`initializeSimlr()`	Initialize simlr
`.int_antsProcessArguments()`	Processing arguments for command line parsing
`integrateVectorField()`	Integrate vector field
`integrateVelocityField()`	integrateVelocityField
`interleaveMatrixWithItself()`	Simple interleaveMatrixWithItself function.
`interpret_simlr_vector()`	Interpret SiMLR Vector
`interpret_simlr_vector2()`	Interpret SiMLR Vector
`invariant_orthogonality_defect()`	Calculate the invariant orthogonality defect that is zero for diagonal matrices
`invertAntsrTransform()`	invertAntsrTransform
`invertDisplacementField()`	invertDisplacementField
`is.antsImage()`	is.antsImage
`jlfProp()`	Propagate Joint Label Fusion (JLF) solutions through a time series
`joinEigenanatomy()`	Simple joinEigenanatomy function.
`jointLabelFusion()`	joint label and intensity fusion
`jointSmoothMatrixReconstruction()`	joint smooth matrix prediction
`kellyKapowski()`	Compute cortical thickness using the DiReCT algorithm.
`kmeansSegmentation()`	k means image segmentation.
`knnSmoothImage()`	k-nearest neighbors constrained image smoothing
`knnSmoothingMatrix()`	k-nearest neighbors constrained smoothing
`labelClusters()`	Simple labelClustering function.
`labelGeometryMeasures()`	labelGeometryMeasures
`labelImageCentroids()`	labelImageCentroids
`labelOverlapMeasures()`	labelOverlapMeasures
`labelStats()`	labelStats
`labels2matrix()`	Convert label image to a matrix
`lappend()`	Simple list append tool
`load.ANTsR()`	Load R sessions with ANTsR objects
`localGyrificationIndex()`	Local gyrification index.
`localJointLabelFusion()`	local joint label and intensity fusion
`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.
`makeImage()`	Simple makeImage function.
`makePointsImage()`	Create label image from physical space points
`makePowersPointsImage()`	Label image from Powers points
`maskImage()`	Mask input image by mask image.
`mask_values()`	Simple Value extractor for antsImage Values
`matrix2timeseries()`	Simple matrix2timeseries function.
`matrixToImages()`	Convert rows of a matrix to images
`mean(<antsImage>)`	Mean for antsImage Objects
`median(<antsImage>)`	Median for antsImage Objects
`mergeChannels()`	merge images into a multiChannel antsImage
`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
`morphology()`	Morphological image operations
`.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
`n3BiasFieldCorrection()`	N3 bias field correction
`n3BiasFieldCorrection2()`	N3 Bias field correction
`n4BiasFieldCorrection()`	N4 bias field correction
`networkEiganat()`	Convenience wrapper for eigenanatomy decomposition.
`orthogonalizeAndQSparsify()`	Sparsify and optionally orthogonalize a matrix
`orthogonalizeAndQSparsifyOld()`	sparsify a matrix
`pairwiseImageDistanceMatrix()`	Simple pairwiseImageDistanceMatrix function for images
`pairwise_matrix_similarity()`	pairwise application of matrix similarity to matrix List projected onto a feature list
`partialVolumeCorrection()`	Perform partial volume correction for ASL images.
`perfusionregression()`	Perfusion Regression
`petSUVR()`	Compute SUVR from PET time series images
`plot(<antsImage>)`	Plotting an image slice or multi-slice with optional color overlay.
`plotBasicNetwork()`	Simple plotBasicNetwork function.
`plotPrettyGraph()`	Simple plotPrettyGraph function saves to png.
`plot_features()`	Plot Features
`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.
`quantile(<antsImage>)`	Sample Quantiles
`randcca()`	randomized cca function.
`randomMask()`	Get a random mask
`randsvd()`	randomized svd function.
`randwhiten()`	randomized whitening function.
`rankBasedMatrixSegmentation()`	rank-based segmentation of a matrix
`rankIntensity()`	rank intensity transformation for an image
`rapidlyInspectImageData()`	Simple rapidlyInspectImageData function.
`readAntsrTransform()`	readAntsrTransform
`readNormalizedPopulationData()`	Read normalized population from h5 file or directory
`read_simlr_data_frames()`	Read a list of data frames from disk with SiMLR-specific naming convention
`reflectImage()`	reflectImage
`reflectionMatrix()`	reflectionMatrix
`regressProjections()`	Regression on image set projection
`regularizeSimlr()`	Automatically produce regularization matrices for simlr
`reho()`	REHO
`renormalizeProbabilityImages()`	Normalize (modified) probability images
`reorientImage()`	reorient image by its principal axis
`resampleImage()`	resampleImage
`resampleImageToTarget()`	resampleImageToTarget
`resels()`	Estimates image resels
`rfSegmentation()`	A rfSegmentation function.
`rfSegmentationPredict()`	A rfSegmentationPredict function.
`rftPval()`	RFT p-values
`rftResults()`	RFT Statistical Results
`ri()`	Minimal function for creating r images
`robustMatrixTransform()`	Simple robustMatrixTransform function.
`rsfDenoise()`	WIP: data-driven denoising for resting state fMRI
`rvcoef()`	RV Coefficient of Two Matrices
`save.ANTsR()`	Save R sessions including ANTsR objects
`sd()`	SD generic
`segmentShapeFromImage()`	convolution-based shape identification
`segmentationRefinement.predict()`	Segmentation refinement using corrective learning (prediction)
`segmentationRefinement.train()`	Segmentation refinement using corrective learning (training)
`setAntsrTransformFixedParameters()`	setAntsrTransformFixedParameters
`setAntsrTransformParameters()`	setAntsrTransformParameters
`shorten_pymm_names()`	shorter antspymm names
`simlr()`	Similarity-driven multiview linear reconstruction model (simlr) for N modalities
`simlr.parameters()`	Generate Parameter Grid for SIMLR Search
`simlr.perm()`	Assess Significance of SiMLR Call
`simlr.search()`	Perform SIMLR Grid Search
`simlrU()`	Compute the low-dimensional u matrix for simlr
`simlr_feature_orth()`	Compute the Average Invariant Orthogonality Defect for Multiple Features
`simlr_impute()`	Impute missing SiMLR data in a specified column based on other columns
`simlr_path_models()`	SiMLR Path Models helper
`simulateDisplacementField()`	simulateDisplacementField
`skeletonize()`	Skeletonize a binary segmentation.
`smoothAppGradCCA()`	cca via sparse smooth matrix prediction
`smoothImage()`	Smooth image
`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.
`splitChannels()`	split a multichannel antsImage
`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.
`subset(<antsImage>)`	Subsetting antsImage Objects
`sum_preserving_matrix_partition()`	Sum preserving matrix partition
`take_abs_unsigned()`	Take Absolute Value of Unsigned Columns
`taskFMRI()`	Simple taskFMRI function.
`temporalwhiten()`	Simple autocorrelation-based temporal whitening function.
`testEanat()`	Test eigenanatomy in order
`thresholdImage()`	Threshold Image
`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).
`unique(<antsImage>)`	Unique for antsImage Objects
`usePkg()`	Use any package. If package is not installed, this will install from CRAN.
`var()`	Variance generic
`vectorToMultichannel()`	Convert vector to multichannel `antsImage`.
`vector_to_df()`	Convert a Vector to a Data Frame
`visualize_lowrank_relationships()`	Visualize Low-Rank Relationships
`visualize_permutation_test()`	Visualize Permutation Test Results
`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.
`whiten_matrix()`	Whitening Matrix
`writeAntsrTransform()`	writeAntsrTransform
`writeNormalizedPopulationData()`	Save normalized population data to a directory or h5 file
`write_simlr_data_frames()`	Write a list of data frames to disk with SiMLR-specific naming convention

Reference

All functions