Man pages for stnava/ANTsR
ANTs in R: Quantification Tools for Biomedical Images
| aal | AAL Labels |
| abpBrainExtraction | An ants-based brain extraction script. |
| abpN4 | MR image bias correction based on the N4 algorithm. |
| accessor-methods | Extract Image Attributes 'pixeltype' from antsImages |
| addNoiseToImage | addNoiseToImage |
| adjusted_rvcoef | Adjusted RV Coefficient |
| affineInitializer | a multi-start optimizer for affine registration |
| alffmap | alffmap |
| 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... |
| antsCompileFlags | return ants compile flags |
| antsCopyImageInfo | Copy header info |
| antsCopyImageInfo2 | Copy header info with different input order |
| antsDir | return ANTs binary directory information |
| antsImage | An S4 class for an antsImage |
| antsImageClone | Clone an 'antsImage'. |
| antsImageGetSet | antsImageGetSet |
| antsImageHeaderInfo | Read file info from image header |
| antsImageIterator | antsImageIterator |
| antsImageIterator_class | An S4 class for an antsImageIterator |
| antsImageIteratorGet | antsImageIteratorGet |
| antsImageIteratorGetIndex | antsImageIteratorGetIndex |
| antsImageIteratorGoToBegin | antsImageIteratorGoToBegin |
| antsImageIteratorGoToReverseBegin | antsImageIteratorGoToReverseBegin |
| antsImageIteratorIsAtEnd | antsImageIteratorIsAtEnd |
| antsImageIteratorIsAtReverseEnd | antsImageIteratorIsAtReverseEnd |
| antsImageIteratorNext | antsImageIteratorNext |
| antsImageIteratorPrevious | antsImageIteratorPrevious |
| antsImageIteratorRemaining | antsImageIteratorRemaining |
| antsImageIteratorSet | antsImageIteratorSet |
| antsImageIteratorSetIndex | antsImageIteratorSetIndex |
| antsImagemath | Math for antsImage Objects |
| antsImageMutualInformation | mutual information between two images |
| antsImageops | Operations for antsImage Objects |
| antsImagePhysicalSpaceConsistency | Check for physical space consistency |
| antsImageRead | Image Read |
| antsImageSummary | Summary for antsImage Objects |
| antsImageTypeCast | Cast images to either a passed pixeltype or the most precise... |
| antsImageWrite | Image Write |
| antsIncludes | return ANTs installation information |
| antsLibs | return ants library location |
| antsMatrix_class | antsMatrix Class |
| antsMotionCalculation | antsMotionCalculation |
| antsMotionCorr | Motion Correction |
| 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 |
| ANTsR | Advanced Normalization Tools in R |
| antsRegion-class | An S4 class to hold a region of an antsImage |
| antsRegistration | Perform registration between two images. |
| antsrGetPointerName | Return the antsImage pointer string |
| antsrimpute | antsrimpute |
| 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. |
| antsrTransform | An S4 class for an antsrTransform |
| antsrTransformFromDisplacementField | antsrTransformFromDisplacementField |
| antsrVersions | antsrVersions |
| antsrVol | Render an image volume with or without overlay. |
| antsSetPixels | Set a pixel value at an index |
| ants.set.seed | Set seed for ANTsR functionality |
| antsSpatialICAfMRI | Perform spatial ICA on fMRI bold data. |
| antsTransformIndexToPhysicalPoint | Get Spatial Point from Index |
| antsTransformPhysicalPointToIndex | Get Index from Spatial Point |
| antsVersions | antsVersions |
| 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... |
| apply_simlr_matrices_dtfix | Apply simlr matrices to an existing data frame and combine... |
| as.antsImage | Convert Objects into antsImage objects |
| as.antsMatrix | Coerce Object to as.antsMatrix |
| as.array | 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 |
| basicInPaint | Inpaints missing imaging data from boundary data |
| ba_svd | No fail SVD function that switches to rsvd if svd fails |
| bayesianCBF | Uses probabilistic segmentation to constrain pcasl-based cbf... |
| bayesianlm | Simple bayesian regression function. |
| bigLMStats | Efficiently compute basic statistical inference from... |
| 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 |
| brackets | Extract or Replace Parts of antsImage Object |
| buildTemplate | ANTs template building. |
| check_ants-methods | 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... |
| decropImage | decrop a sub-image back into the full image |
| denoiseImage | Denoise an image |
| density.antsImage | Density of Values in an Image |
| DesikanKillianyTourville | DesikanKillianyTourville |
| 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... |
| exploratory_visualization | Exploratory Clustering and Visualization |
| extractSlice | extract a slice from an image |
| fastMarchingExtension | Fast Marching Extension filter will extend an intensity or... |
| filterfMRIforNetworkAnalysis | Basic pre-processing for BOLD or ASL-based network analysis. |
| fitBsplineDisplacementField | fitBsplineDisplacementField |
| fitBsplineObjectToScatteredData | fitBsplineObjectToScatteredData |
| fitThinPlateSplineDisplacementField | fitThinPlateSplineDisplacementField |
| fitTimeVaryingTransformToPointSets | fitTimeVaryingTransformToPointSets |
| fitTransformToPairedPoints | fitTransformToPairedPoints |
| fMRINormalization | Multi-run normalization, filtering and nuisance estimation... |
| frequencyFilterfMRI | Band pass filtering for BOLD image. |
| fsl2antsrTransform | fsl2antsrTransform |
| functionalLungSegmentation | Ventilation-based segmentation of hyperpolarized gas lung... |
| fuzzySpatialCMeansSegmentation | fuzzySpatialCMeansSegmentation |
| generateAifMaskImage | Automatically generate an arterial input function mask. |
| geoSeg | brain segmentation based on geometric priors |
| getANTsRData | getANTsRData |
| getAntsrTransformFixedParameters | getAntsrTransformFixedParameters |
| getAntsrTransformParameters | getAntsrTransformParameters |
| getASLNoisePredictors | Get nuisance predictors from ASL images |
| getAverageOfTimeSeries | getAverageOfTimeSeries |
| getCenterOfMass | center of mass |
| getCentroids | Convert an image to the geometric centroids of its signal |
| getfMRInuisanceVariables | Extract generic fMRI nuisance variables for ASL or BOLD |
| getMask | Get Mask |
| getMultiResFeatureMatrix | build multiple resolution predictor matrix from feature... |
| getMultivariateTemplateCoordinates | Label multivariate components by an anatomical coordinate... |
| 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... |
| 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 |
| grapes-greater-than-grapes | 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 |
| icawhiten | Simple icawhitening function. |
| ilr | Efficiently compute an image-based linear regression model... |
| 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 |
| iMath | iMath |
| iMathOps | Operations for iMath Operator |
| indicator_opt_both_ways | Helper Function to Optimize Indicator Matrix with Best Sum |
| initializeEigenanatomy | Convert a matrix to a form that can be used to initialize... |
| 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... |
| invertAntsrTransform | invertAntsrTransform |
| invertDisplacementField | invertDisplacementField |
| is.antsImage | is.antsImage |
| jlfProp | Propagate Joint Label Fusion (JLF) solutions through a time... |
| 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 |
| labelImageRegistration | Perform label image registration. |
| labelOverlapMeasures | labelOverlapMeasures |
| labels2matrix | Convert label image to a matrix |
| labelStats | labelStats |
| 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... |
| 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 | Mean for antsImage Objects |
| median | Median for antsImage Objects |
| mergeChannels | merge images into a multiChannel antsImage |
| mergeListToNDImage | mergeListToNDImage |
| mild | Efficiently compute a multivariate, image-based (mixed)... |
| milr | Efficiently compute a multivariate, penalized image-based... |
| 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... |
| mrvnrfs.predict | multi-res voxelwise neighborhood random forest segmentation |
| multichannelPCA | Shape analysis of multichannel images based on PCA |
| multichannelToVector | Convert multichannel 'antsImage' to a vector. |
| multiLabelMorphology | Morphology on multi label images. |
| multiResRandomForestRegression | multiple resolution neighborhood random forest regression |
| multiscaleSVD | Multi-scale svd |
| multiview_pca | Multiview PCA |
| n3BiasFieldCorrection | N3 bias field correction |
| n3BiasFieldCorrection2 | N3 Bias field correction |
| n4BiasFieldCorrection | N4 bias field correction |
| networkEiganat | Convenience wrapper for eigenanatomy decomposition. |
| optimize_indicator_matrix | Optimize Binary Indicator Matrix with Row Uniformity |
| 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... |
| 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... |
| plotBasicNetwork | Simple plotBasicNetwork function. |
| plot_features | Plot Features |
| plotPrettyGraph | Simple plotPrettyGraph function saves to png. |
| powers_areal_mni_itk | powers_areal_mni_itk |
| predictSimlr | predict output matrices from simlr solution |
| preprocessfMRI | Preprocess BOLD fMRI image data. |
| preprocessRestingBOLD | Preprocess resting 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... |
| 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 |
| segmentationRefinement.predict | Segmentation refinement using corrective learning... |
| segmentationRefinement.train | Segmentation refinement using corrective learning (training) |
| segmentShapeFromImage | convolution-based shape identification |
| setAntsrTransformFixedParameters | setAntsrTransformFixedParameters |
| setAntsrTransformParameters | setAntsrTransformParameters |
| shorten_pymm_names | shorter antspymm names |
| simlr | Similarity-driven multiview linear reconstruction model... |
| simlr_feature_orth | Compute the Average Invariant Orthogonality Defect for... |
| simlr_impute | Impute missing SiMLR data in a specified column based on... |
| simlr.parameters | Generate Parameter Grid for SIMLR Search |
| simlr_path_models | SiMLR Path Models helper |
| simlr.perm | Assess Significance of SiMLR Call |
| simlr.search | Perform SIMLR Grid Search |
| simlrU | Compute the low-dimensional u matrix for simlr |
| 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... |
| 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... |
| sparseDecomboot | Convenience wrapper for eigenanatomy decomposition. |
| sparseDistanceMatrix | Create sparse distance, covariance or correlation matrix |
| sparseDistanceMatrixXY | Create sparse distance, covariance or correlation matrix from... |
| 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... |
| subgradientL1Regression | Simple subgradientL1Regression function. |
| subjectDataToGroupDataFrame | convert subject matrix data to a row in a dataframe. |
| subset | 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... |
| tracts | tracts |
| trapz | Calculate the area under a sampled curve (or set of curves). |
| unique | Unique for antsImage Objects |
| usePkg | Use any package. If package is not installed, this will... |
| var | Variance generic |
| vector_to_df | Convert a Vector to a Data Frame |
| vectorToMultichannel | Convert vector to multichannel 'antsImage'. |
| visualize_lowrank_relationships | Visualize Low-Rank Relationships |
| visualize_permutation_test | Visualize Permutation Test Results |
| vwnrfs | voxelwise neighborhood random forest segmentation and... |
| 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... |
