Man pages for neuroconductor-devel/ANTsR
ANTs in R: Quantification Tools for Biomedical Images

aalaal
abpBrainExtractionAn ants-based brain extraction script.
abpN4MR image bias correction based on the N4 algorithm.
affineInitializera multi-start optimizer for affine registration
alffmapalffmap
antsBOLDNetworkAnalysisa basic framework for network analysis that produces graph...
antsMotionCalculationantsMotionCalculation
antsMotionCorrMotion Correction
antsrMotionCalculationantsrMotionCalculation
antsrSurfRender a function onto a surface.
antsrVersionsantsrVersions
antsrVolRender an image volume with or without overlay.
antsSpatialICAfMRIPerform spatial ICA on fMRI bold data.
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.
basicInPaintInpaints missing imaging data from boundary data
bayesianCBFUses probabilistic segmentation to constrain pcasl-based cbf...
bayesianlmSimple bayesian regression function.
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.
composeTransformsToFieldCompose arbitrary transform list into a deformation field.
computeDVARScomputeDVARS
computeDVARSspatialMapcomputeDVARSspatialMap
convolveImageconvolve one image with another
corwproduces a correlation matrix via weighted correlation.
createJacobianDeterminantImagecreateJacobianDeterminantImage
createWarpedGridCreate a warped grid for visualization.
crossvalidatedR2Cross-Validated R^2 value
cvEigenanatomyCross-validation method for eigenanatomy decompositions.
deconvolutionSVDRegularize SVD (deconvolution) solution of cerebral blood...
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...
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
getASLNoisePredictorsGet nuisance predictors from ASL images
getAverageOfTimeSeriesgetAverageOfTimeSeries
getCenterOfMasscenter of mass
getfMRInuisanceVariablesExtract generic fMRI nuisance variables for ASL or BOLD
getMultiResFeatureMatrixbuild multiple resolution predictor matrix from feature...
getMultivariateTemplateCoordinatesLabel multivariate components by an anatomical coordinate...
getTemplateCoordinatesDefine an anatomical coordinate system in a new image based...
hemodynamicRFLinear Model for FMRI Data
histogramMatchImagehistogramMatchImage
icawhitenSimple icawhitening function.
image2ClusterImagesConverts an image to several independent images.
imageDomainToSpatialMatrixImage domain to spatial position
initializeEigenanatomyConvert a matrix to a form that can be used to initialize...
interleaveMatrixWithItselfSimple interleaveMatrixWithItself function.
invariantImageSimilaritysimilarity metrics between two images as a function of...
jlfPropPropagate Joint Label Fusion (JLF) solutions through a time...
joinEigenanatomySimple joinEigenanatomy function.
jointSmoothMatrixReconstructionjoint smooth matrix prediction
kellyKapowskiCompute cortical thickness using the DiReCT algorithm.
knnSmoothImagek-nearest neighbors constrained image smoothing
knnSmoothingMatrixk-nearest neighbors constrained smoothing
labelGeometryMeasureslabelGeometryMeasures
labelImageCentroidslabelImageCentroids
labels2matrixConvert label image to a matrix
load.ANTsRLoad R sessions with ANTsR objects
localGyrificationIndexLocal gyrification index.
lowrankRowMatrixProduces a low rank version of the input matrix
make3ViewPNGRotate an existing 3d window into different views.
makeGraphSimple function to create and measure a graph from a square...
makePointsImageCreate label image from physical space points
makePowersPointsImageLabel image from Powers points
matrix2timeseriesSimple matrix2timeseries function.
mergeListToNDImagemergeListToNDImage
mildEfficiently compute a multivariate, image-based (mixed)...
milrEfficiently compute a multivariate, penalized image-based...
milr.predictPredict from a milr output
mni2talBrett's mni2tal
motion_correctionSimple motion_correction function.
mrvnrfsmulti-res voxelwise neighborhood random forest segmentation...
mrvnrfs.predictmulti-res voxelwise neighborhood random forest segmentation
multichannelPCAShape analysis of multichannel images based on PCA
multichannelToVectorConvert multichannel 'antsImage' to a vector.
multiLabelMorphologyMorphology on multi label images.
multiResRandomForestRegressionmultiple resolution neighborhood random forest regression
multiscaleSVDMulti-scale svd
networkEiganatConvenience wrapper for eigenanatomy decomposition.
orthogonalizeAndQSparsifysparsify a matrix
pairwiseImageDistanceMatrixSimple pairwiseImageDistanceMatrix function for images
partialVolumeCorrectionPerform partial volume correction for ASL images.
perfusionregressionPerfusion Regression
petSUVRCompute SUVR from PET time series images
plotBasicNetworkSimple plotBasicNetwork function.
plotPrettyGraphSimple plotPrettyGraph function saves to png.
powers_areal_mni_itkpowers_areal_mni_itk
preprocessfMRIPreprocess BOLD fMRI image data.
preprocessRestingBOLDPreprocess resting BOLD fMRI image data.
priorBasedSegmentationspatial prior-based image segmentation.
quantifyCBFquantifyCBF
quantifySNPsSimple quantifySNPs function.
randccarandomized cca function.
randsvdrandomized svd function.
randwhitenrandomized whitening function.
rapidlyInspectImageDataSimple rapidlyInspectImageData function.
readNormalizedPopulationDataRead normalized population from h5 file or directory
reexportsObjects exported from other packages
reflectImagereflectImage
regressionNetworkVizVisualize a regression result by a d3 network visualization.
regressProjectionsRegression on image set projection
rehoREHO
renderImageLabels3D surface-based rendering of image segmentation labels
renderSurfaceFunction3D surface-based rendering of volume images.
renormalizeProbabilityImagesNormalize (modified) probability images
reorientImagereorient image by its principal axis
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 R sessions including ANTsR objects
segmentationRefinement.predictSegmentation refinement using corrective learning...
segmentationRefinement.trainSegmentation refinement using corrective learning (training)
segmentShapeFromImageconvolution-based shape identification
skeletonizeSkeletonize a binary segmentation.
smoothAppGradCCAcca via sparse smooth matrix prediction
smoothMatrixPredictionsmooth matrix prediction
smoothMultiRegressionReconstruct a n by k vector given n by p matrix of...
smoothRegressionsmooth matrix-based regression
sparseDecomConvenience wrapper for eigenanatomy decomposition.
sparseDecom2Convenience wrapper for 2-view eigenanatomy decomposition.
sparseDecom2bootConvenience wrapper for 2-view eigenanatomy decomposition...
sparseDecombootConvenience wrapper for eigenanatomy decomposition.
sparseDistanceMatrixCreate sparse distance, covariance or correlation matrix
sparseDistanceMatrixXYCreate sparse distance, covariance or correlation matrix from...
sparseRegressionSparse regression on input images.
spatialbayesianlmspatially constrained bayesian regression function.
splitDataSplit data for testing and training
splitMasksplit a mask into n labeled sub-masks
splitNDImageToListsplitNDImageToList
statFieldThreshProduces a threshold value based on cluster or voxel level...
subgradientL1RegressionSimple subgradientL1Regression function.
subjectDataToGroupDataFrameconvert subject matrix data to a row in a dataframe.
symilrSymmetric multivariate, penalized image-based linear...
symilr2Symmetric multivariate, penalized image-based linear...
symilrUCompute the low-dimensional u matrix for symilr
taskFMRISimple taskFMRI function.
temporalwhitenSimple autocorrelation-based temporal whitening function.
testEanatTest eigenanatomy in order
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).
vectorToMultichannelConvert vector to multichannel 'antsImage'.
vwnrfsvoxelwise neighborhood random forest segmentation and...
vwnrfs.predictvoxelwise neighborhood random forest prediction
weingartenImageCurvatureimage curvature for 2D or 3D
whitenSimple whitening function.
writeNormalizedPopulationDataSave normalized population data to a directory or h5 file
neuroconductor-devel/ANTsR documentation built on Oct. 18, 2019, 4:30 a.m.