Man pages for muschellij2/ANTsR_norgl
ANTs in R

aalaal
abpBrainExtractionAn ants-based brain extraction script.
abpN4MR image bias correction based on the N4 algorithm.
affineInitializera multi-start optimizer for affine registration
alffmapalffmap
antsApplyTransformsApply transforms to images.
antsApplyTransformsToPointsApply transforms to points.
antsAverageImagesComputes average of image list
antsBOLDNetworkAnalysisa basic framework for network analysis that produces graph...
antsCopyImageInfoCopy header info
antsImageAritharith.antsImage
antsImage-classAn S4 class for an antsImage
antsImageCloneClone an 'antsImage'.
antsImageGetSetantsImageGetSet
antsImageHeaderInfoRead file info from image header
antsImageIteratorantsImageIterator
antsImageIterator-classAn S4 class for an antsImageIterator
antsImageIteratorGetantsImageIteratorGet
antsImageIteratorGetIndexantsImageIteratorGetIndex
antsImageIteratorGoToBeginantsImageIteratorGoToBegin
antsImageIteratorGoToReverseBeginantsImageIteratorGoToReverseBegin
antsImageIteratorIsAtEndantsImageIteratorIsAtEnd
antsImageIteratorIsAtReverseEndantsImageIteratorIsAtReverseEnd
antsImageIteratorNextantsImageIteratorNext
antsImageIteratorPreviousantsImageIteratorPrevious
antsImageIteratorRemainingantsImageIteratorRemaining
antsImageIteratorSetantsImageIteratorSet
antsImageIteratorSetIndexantsImageIteratorSetIndex
antsImageMutualInformationmutual information between two images
antsImagePhysicalSpaceConsistencyCheck for physical space consistency
antsImageReadImage Read
antsImageWriteImage Write
antsMatrix-classAn S4 class to hold an antsMatrix imported from ITK types C++...
antsMotionCalculationantsMotionCalculation
antsMotionCorrMotion Correction
antsRegion-classAn S4 class to hold a region of an antsImage
antsRegistrationPerform registration between two images.
antsrGetPointerNameReturn the antsImage pointer string
antsrimputeantsrimpute
antsrMotionCalculationantsrMotionCalculation
antsrSurfRender a function onto a surface.
antsrTransform-classAn S4 class for an antsrTransform
antsSetPixelsSet a pixel value at an index
antsSpatialICAfMRIPerform spatial ICA on fMRI bold data.
antsTransformIndexToPhysicalPointGet Spatial Point from Index
antsTransformPhysicalPointToIndexGet Index from Spatial Point
apply.antsImageExtension of apply to allow input of antsImage
applyAntsrTransformapplyAntsrTransform
applyAntsrTransformToImageapplyAntsrTransformToImage
applyAntsrTransformToPointapplyAntsrTransformToPoint
applyAntsrTransformToVectorapplyAntsrTransformToVector
as.antsImageas.antsImage
as.antsMatrixas.antsMatrix
aslAveragingAverage ASL tag-control pairs to estimate perfusion
aslCensoringCensor bad volumes from ASL data.
aslDenoiseRWIP: data-driven denoising for ASL MRI
aslPerfusionASL-based Perfusion from PASL, CASL or pCASL.
atroposFMM Segmentation
basicInPaintInpaints missing imaging data from boundary data
bayesianCBFUses probabilistic segmentation to constrain pcasl-based cbf...
bayesianlmSimple bayesian regression function.
bigLMStatsEfficiently compute basic statistical inference from...
blockStimulusBlock stimulus model for FMRI Data
bloodPerfusionSVDCalculate blood perfusion using deconvolution.
bold_correlation_matrixbold_correlation_matrix
clusterTimeSeriesSplit time series image into k distinct images
combineNuisancePredictorsCombine and reduce dimensionality of nuisance predictors.
compcorCompcors the input matrix using SVD and returns the result.
composeAntsrTransformscomposeAntsrTransforms
computeDVARScomputeDVARS
computeDVARSspatialMapcomputeDVARSspatialMap
convolveImageconvolve one image with another
corwproduces a correlation matrix via weighted correlation.
createAntsrTransformcreateAntsrTransform
createJacobianDeterminantImagecreateJacobianDeterminantImage
cropImagecrop a sub-image via a mask
cropIndicescrop a sub-image by image indices
crossvalidatedR2Cross-Validated R^2 value
cvEigenanatomyCross-validation method for eigenanatomy decompositions.
deconvolutionSVDRegularize SVD (deconvolution) solution of cerebral blood...
decropImagedecrop a sub-image back into the full image
DesikanKillianyTourvilleDesikanKillianyTourville
eanatDefEigenanatomy with deflation
eanatSelectSelection of n eigenvectors and sparsity for eigenanatomy
eigSegSegmentation for eigenanatomy.
estSmoothEstimate image smoothness
eulerEuler Character
exemplarInpaintingUses example images to inpaint or approximate an existing...
extractSliceextract a slice from an image
fastMarchingExtensionFast Marching Extension filter will extend an intensity or...
filterfMRIforNetworkAnalysisBasic pre-processing for BOLD or ASL-based network analysis.
fMRINormalizationMulti-run normalization, filtering and nuisance estimation...
frequencyFilterfMRIBand pass filtering for BOLD image.
fsl2antsrTransformfsl2antsrTransform
geoSegbrain segmentation based on geometric priors
getANTsRDatagetANTsRData
getAntsrTransformFixedParametersgetAntsrTransformParameters
getAntsrTransformParametersgetAntsrTransformParameters
getASLNoisePredictorsGet nuisance predictors from ASL images
getAverageOfTimeSeriesgetAverageOfTimeSeries
getCentroidsConvert an image to the geometric centroids of its signal
getfMRInuisanceVariablesExtract generic fMRI nuisance variables for ASL or BOLD
getMaskGet Mask
getMultiResFeatureMatrixbuild multiple resolution predictor matrix from feature...
getMultivariateTemplateCoordinatesLabel multivariate components by an anatomical coordinate...
getNeighborhoodAtVoxelGet a hypercube neighborhood at a voxel
getNeighborhoodInMaskGet neighborhoods for voxels within mask
getPixelsGet Pixels
getTemplateCoordinatesDefine an anatomical coordinate system in a new image based...
grapes-greater-than-grapesPipe an object forward
hemodynamicRFLinear Model for FMRI Data
iBindiBind
icawhitenSimple icawhitening function.
image2ClusterImagesConverts an image to several independent images.
imageFileNames2ImageListSimple imageFileNames2ImageListing function.
imageListToMatrixRead Images into a Matrix
imagesToMatrixRead Images into a Matrix
iMathiMath
iMathOpsiMathOps
initializeEigenanatomyConvert a matrix to a form that can be used to initialize...
interleaveMatrixWithItselfSimple interleaveMatrixWithItself function.
invariantImageSimilaritysimilarity metrics between two images as a function of...
invertAntsrTransforminvertAntsrTransform
is.antsImageis.antsImage
joinEigenanatomySimple joinEigenanatomy function.
jointIntensityFusionjoint intensity fusion
jointIntensityFusion3DjointIntensityFusion3D
jointLabelFusionjoint label fusion
jointLabelFusion3DjointLabelFusion3D
kellyKapowskiCompute cortical thickness using the DiReCT algorithm.
kmeansSegmentationk means image segmentation.
labelClustersSimple labelClustering function.
labelGeometryMeasureslabelGeometryMeasures
labelImageCentroidslabelImageCentroids
labels2matrixConvert label image to a matrix
labelStatslabelStats
lappendSimple list append tool
lowrankRowMatrixProduces a low rank version of the input matrix
makeGraphSimple function to create and measure a graph from a square...
makeImageSimple makeImage function.
makePointsImageCreate label image from physical space points
makePowersPointsImageLabel image from Powers points
maskImageMask input image by mask image.
matrix2timeseriesSimple matrix2timeseries function.
matrixToImagesConvert rows of a matrix to images
mergeChannelsmerge images into a multiChannel antsImage
mni2talBrett's mni2tal
morphologyMorphological image operations
mrvnrfsmulti-res voxelwise neighborhood random forest segmentation...
mrvnrfs.predictmulti-res voxelwise neighborhood random forest segmentation
multiLabelMorphologyMorphology on multi label images.
multiResRandomForestRegressionmultiple resolution neighborhood random forest regression
n3BiasFieldCorrectionBias Field Correction
n4BiasFieldCorrectionBias Field Correction
networkEiganatConvenience wrapper for eigenanatomy decomposition.
pairwiseImageDistanceMatrixSimple pairwiseImageDistanceMatrix function for images
partialVolumeCorrectionPerform partial volume correction for ASL images.
perfusionregressionPerfusion Regression
petSUVRCompute SUVR from PET time series images
plot.antsImagePlotting an image slice or multi-slice with optional color...
plotPrettyGraphSimple plotPrettyGraph function saves to png.
powers_areal_mni_itkpowers_areal_mni_itk
preprocessfMRIPreprocess BOLD fMRI image data.
preprocessRestingBOLDPreprocess resting BOLD fMRI image data.
quantifyCBFquantifyCBF
quantifySNPsSimple quantifySNPs function.
randccarandomized cca function.
randomMaskGet a random mask
randsvdrandomized svd function.
randwhitenrandomized whitening function.
rapidlyInspectImageDataSimple rapidlyInspectImageData function.
readAntsrTransformreadAntsrTransform
readNormalizedPopulationDataRead normalized population from h5 file
reflectImagereflectImage
regressionNetworkVizVisualize a regression result by a d3 network visualization.
regressProjectionsRegression on image set projection
rehoREHO
renormalizeProbabilityImagesNormalize (modified) probability images
reorientImagereorient image by its principal axis
resampleImageresampleImage
resampleImageToTargetresampleImageToTarget
reselsEstimates image resels
rfSegmentationA rfSegmentation function.
rfSegmentationPredictA rfSegmentationPredict function.
rftPvalRFT p-values
rftResultsRFT Statistical Results
robustMatrixTransformSimple robustMatrixTransform function.
rsfDenoiseWIP: data-driven denoising for resting state fMRI
save.ANTsRsave.ANTsR
segmentationRefinement.predictSegmentation refinement using corrective learning...
segmentationRefinement.trainSegmentation refinement using corrective learning (training)
segmentShapeFromImageconvolution-based shape identification
setAntsrTransformFixedParameterssetAntsrTransformParameters
setAntsrTransformParameterssetAntsrTransformParameters
smoothImageSmooth image
sparseDecomConvenience wrapper for eigenanatomy decomposition.
sparseDecom2Convenience wrapper for 2-view eigenanatomy decomposition.
sparseDecom2bootConvenience wrapper for 2-view eigenanatomy decomposition...
sparseDecombootConvenience wrapper for eigenanatomy decomposition.
sparseRegressionSparse regression on input images.
spatialbayesianlmspatially constrained bayesian regression function.
splitChannelssplit a multichannel antsImage
splitDataSplit data for testing and training
splitMasksplit a mask into n labeled sub-masks
statFieldThreshProduces a threshold value based on cluster or voxel level...
sub-antsImage-NULL-ANY-methodants image substitutions
subgradientL1RegressionSimple subgradientL1Regression function.
subjectDataToGroupDataFrameconvert subject matrix data to a row in a dataframe.
taskFMRISimple taskFMRI function.
temporalwhitenSimple autocorrelation-based temporal whitening function.
testEanatTest eigenanatomy in order
thresholdImageThreshold Image
timeseries2matrixTime-series image to matrix
timeseriesN3Run N3 on slices of timeseries.
timeserieswindow2matrixTime-series image to matrix of time windows around...
tractstracts
trapzCalculate the area under a sampled curve (or set of curves).
usePkgUse any package. If package is not installed, this will...
vwnrfsvoxelwise neighborhood random forest segmentation and...
vwnrfs.predictvoxelwise neighborhood random forest prediction
weingartenImageCurvatureimage curvature for 3D
whitenSimple whitening function.
writeAntsrTransformwriteAntsrTransform
writeNormalizedPopulationDataSave normalized population data to a h5 file
muschellij2/ANTsR_norgl documentation built on May 22, 2017, 4:22 p.m.