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 |