All functions

pixeltype() `pixeltype<-`() components() `components<-`() spacing() `spacing<-`() direction() `direction<-`() origin() `origin<-`()

Extract Image Attributes pixeltype from antsImages

ants.set.seed()

Set seed for ANTsR functionality

antsApplyTransforms()

Apply transforms to images.

antsApplyTransformsToPoints()

Apply transforms to points.

antsAverageImages()

Computes average of image list

antsCompileFlags()

return ants compile flags

antsCopyImageInfo()

Copy header info

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>) 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

which(<antsImage>) 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>) `&`(<antsImage>,<antsImage>) `|`(<antsImage>,<antsImage>) Logic(<antsImage>,<array>) Logic(<array>,<antsImage>) `&`(<antsImage>,<logical>) `|`(<antsImage>,<logical>) Logic(<logical>,<antsImage>) Logic(<antsImage>,<numeric>) Logic(<numeric>,<antsImage>) Logic(<antsImage>,<ANY>) Logic(<ANY>,<antsImage>) Logic(<list>,<antsImage>) Logic(<antsImage>,<list>)

Operations for antsImage Objects

antsIncludes()

return ANTs installation information

antsLibs()

return ants library location

initialize(<antsMatrix>)

antsMatrix Class

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

antsTransformIndexToPhysicalPoint()

Get Spatial Point from Index

antsTransformPhysicalPointToIndex()

Get Index from Spatial Point

antsVersions

antsVersions

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

show(<antsrTransform>) initialize(<antsrTransform>)

An S4 class for an antsrTransform

antsrTransformFromDisplacementField()

antsrTransformFromDisplacementField

antsrimpute()

antsrimpute

apply()

Extension of apply to allow input of antsImage

applyAntsrTransform()

applyAntsrTransform

applyAntsrTransformToImage()

applyAntsrTransformToImage

applyAntsrTransformToPoint()

applyAntsrTransformToPoint

applyAntsrTransformToVector()

applyAntsrTransformToVector

as.antsImage()

Convert Objects into antsImage objects

as.antsMatrix()

Coerce Object to as.antsMatrix

dim(<antsImage>) is.na(<antsImage>) as.numeric(<antsImage>) as.matrix(<antsImage>) as.matrix(<antsImage>) as.array(<antsImage>) as.array(<antsImage>) as.character(<antsImage>) as.factor(<antsImage>) factor(<antsImage>) as.data.frame(<antsMatrix>) as.data.frame(<antsMatrix>) as.matrix(<antsMatrix>) as.list(<antsMatrix>)

Coerce antsImage objects to array

atropos()

FMM Segmentation

bigLMStats()

Efficiently compute basic statistical inference from regressions with multiple outcomes

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>,<logical>,<ANY>,<ANY>) `[`(<antsImage>,<ANY>,<ANY>,<ANY>) `[`(<antsImage>,<ANY>,<ANY>,<ANY>) `[`(<antsImage>,<NULL>,<NULL>,<ANY>) `[`(<antsImage>,<NULL>,<NULL>,<ANY>) `[`(<antsImage>,<numeric>,<numeric>,<ANY>) `[`(<antsImage>,<numeric>,<numeric>,<ANY>) `[`(<antsImage>,<numeric>,<NULL>,<ANY>) `[`(<antsImage>,<numeric>,<NULL>,<ANY>) `[`(<antsImage>,<NULL>,<numeric>,<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

coerce_mask()

Simple Mask Maker

composeAntsrTransforms()

composeAntsrTransforms

createAntsrTransform()

createAntsrTransform

cropImage()

crop a sub-image via a mask

cropIndices()

crop a sub-image by image indices

cut(<antsImage>)

Perform Cut on an image

decropImage()

decrop a sub-image back into the full image

denoiseImage()

Denoise an image

density(<antsImage>)

Density of Values in an Image

displacementFieldFromAntsrTransform()

displacementFieldFromAntsrTransform

error_not_antsImage()

Stop if not an antsImage object

extractSlice()

extract a slice from an image

getANTsRData()

getANTsRData

getAntsrTransformFixedParameters()

getAntsrTransformFixedParameters

getAntsrTransformParameters()

getAntsrTransformParameters

getCentroids()

Convert an image to the geometric centroids of its signal

getMask()

Get Mask

getNeighborhoodAtVoxel()

Get a hypercube neighborhood at a voxel

getNeighborhoodInMask()

Get neighborhoods for voxels within mask

getPixels()

Get Pixels

`%>%`

Pipe an object forward

hist(<antsImage>)

Histogram of Values in an Image

iBind()

iBind

iMath()

iMath

iMathOps

Operations for iMath Operator

ilr()

Efficiently compute an image-based linear regression model (ilr)

ilr.predict()

Predict from ilr output

imageFileNames2ImageList()

Simple imageFileNames2ImageListing function.

imageListToMatrix()

Read Images into a Matrix

imageSimilarity()

imageSimilarity

imagesToMatrix()

Read Images into a Matrix

.int_antsProcessArguments()

Processing arguments for command line parsing

invertAntsrTransform()

invertAntsrTransform

is.antsImage()

is.antsImage

jointLabelFusion()

joint label and intensity fusion

kmeansSegmentation()

k means image segmentation.

labelClusters()

Simple labelClustering function.

labelStats()

labelStats

lappend()

Simple list append tool

makeImage()

Simple makeImage function.

maskImage()

Mask input image by mask image.

mask_values()

Simple Value extractor for antsImage Values

matrixToImages()

Convert rows of a matrix to images

mean(<antsImage>) sd.antsImage()

Mean for antsImage Objects

median(<antsImage>)

Median for antsImage Objects

mergeChannels()

merge images into a multiChannel antsImage

morphology()

Morphological image operations

n3BiasFieldCorrection()

Bias Field Correction

n4BiasFieldCorrection()

Bias Field Correction

plot(<antsImage>)

Plotting an image slice or multi-slice with optional color overlay.

quantile(<antsImage>)

Sample Quantiles

randomMask()

Get a random mask

readAntsrTransform()

readAntsrTransform

resampleImage()

resampleImage

resampleImageToTarget()

resampleImageToTarget

ri()

Minimal function for creating r images

ripmmarc()

Rotation Invariant Patch-based Multi-Modality Analysis aRChitecture

ripmmarcBasisImage()

Generate an antsImage from ripmmarc basis data

ripmmarcPop()

RIPMMARC population basis

setAntsrTransformFixedParameters()

setAntsrTransformFixedParameters

setAntsrTransformParameters()

setAntsrTransformParameters

smoothImage()

Smooth image

splitChannels()

split a multichannel antsImage

subset(<antsImage>)

Subsetting antsImage Objects

thresholdImage()

Threshold Image

unique(<antsImage>)

Unique for antsImage Objects

usePkg()

Use any package. If package is not installed, this will install from CRAN.

var()

Variance generic

writeAntsrTransform()

writeAntsrTransform