Man pages for neuroconductor/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. |
| addNoiseToImage | addNoiseToImage |
| affineInitializer | a multi-start optimizer for affine registration |
| alffmap | alffmap |
| antsBOLDNetworkAnalysis | a basic framework for network analysis that produces graph... |
| antsMotionCalculation | antsMotionCalculation |
| antsMotionCorr | Motion Correction |
| antsrMotionCalculation | antsrMotionCalculation |
| antsrSurf | Render a function onto a surface. |
| antsrVersions | antsrVersions |
| antsrVol | Render an image volume with or without overlay. |
| antsSpatialICAfMRI | Perform spatial ICA on fMRI bold data. |
| 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. |
| basicInPaint | Inpaints missing imaging data from boundary data |
| bayesianCBF | Uses probabilistic segmentation to constrain pcasl-based cbf... |
| bayesianlm | Simple bayesian regression function. |
| blockStimulus | Block stimulus model for FMRI Data |
| bloodPerfusionSVD | Calculate blood perfusion using deconvolution. |
| bold_correlation_matrix | BOLD Correlation Matrix |
| clusterTimeSeries | Split time series image into k distinct images |
| combineNuisancePredictors | Combine and reduce dimensionality of nuisance predictors. |
| compcor | Compcors the input matrix using SVD and returns the result. |
| 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. |
| createJacobianDeterminantImage | createJacobianDeterminantImage |
| createWarpedGrid | Create a warped grid for visualization. |
| crossvalidatedR2 | Cross-Validated R^2 value |
| cvEigenanatomy | Cross-validation method for eigenanatomy decompositions. |
| deconvolutionSVD | Regularize SVD (deconvolution) solution of cerebral blood... |
| DesikanKillianyTourville | DesikanKillianyTourville |
| eanatDef | Eigenanatomy with deflation |
| eanatSelect | Selection of n eigenvectors and sparsity for eigenanatomy |
| eigSeg | Segmentation for eigenanatomy. |
| estSmooth | Estimate image smoothness |
| euler | Euler Character |
| exemplarInpainting | Uses example images to inpaint or approximate an existing... |
| fastMarchingExtension | Fast Marching Extension filter will extend an intensity or... |
| filterfMRIforNetworkAnalysis | Basic pre-processing for BOLD or ASL-based network analysis. |
| fitBsplineObjectToScatteredData | fitBsplineObjectToScatteredData |
| 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... |
| generateAifMaskImage | Automatically generate an arterial input function mask. |
| geoSeg | brain segmentation based on geometric priors |
| getASLNoisePredictors | Get nuisance predictors from ASL images |
| getAverageOfTimeSeries | getAverageOfTimeSeries |
| getCenterOfMass | center of mass |
| getfMRInuisanceVariables | Extract generic fMRI nuisance variables for ASL or BOLD |
| getMultiResFeatureMatrix | build multiple resolution predictor matrix from feature... |
| getMultivariateTemplateCoordinates | Label multivariate components by an anatomical coordinate... |
| getTemplateCoordinates | Define an anatomical coordinate system in a new image based... |
| hemodynamicRF | Linear Model for FMRI Data |
| histogramMatchImage | histogramMatchImage |
| icawhiten | Simple icawhitening function. |
| image2ClusterImages | Converts an image to several independent images. |
| imageDomainToSpatialMatrix | Image domain to spatial position |
| initializeEigenanatomy | Convert a matrix to a form that can be used to initialize... |
| initializeSimlr | Initialize simlr |
| interleaveMatrixWithItself | Simple interleaveMatrixWithItself function. |
| invariantImageSimilarity | similarity metrics between two images as a function of... |
| jlfProp | Propagate Joint Label Fusion (JLF) solutions through a time... |
| joinEigenanatomy | Simple joinEigenanatomy function. |
| jointSmoothMatrixReconstruction | joint smooth matrix prediction |
| kellyKapowski | Compute cortical thickness using the DiReCT algorithm. |
| knnSmoothImage | k-nearest neighbors constrained image smoothing |
| knnSmoothingMatrix | k-nearest neighbors constrained smoothing |
| labelGeometryMeasures | labelGeometryMeasures |
| labelImageCentroids | labelImageCentroids |
| labelOverlapMeasures | labelOverlapMeasures |
| labels2matrix | Convert label image to a matrix |
| load.ANTsR | Load R sessions with ANTsR objects |
| localGyrificationIndex | Local gyrification index. |
| 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... |
| makePointsImage | Create label image from physical space points |
| makePowersPointsImage | Label image from Powers points |
| matrix2timeseries | Simple matrix2timeseries function. |
| 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 |
| 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 |
| networkEiganat | Convenience wrapper for eigenanatomy decomposition. |
| orthogonalizeAndQSparsify | sparsify a matrix |
| pairwiseImageDistanceMatrix | Simple pairwiseImageDistanceMatrix function for images |
| partialVolumeCorrection | Perform partial volume correction for ASL images. |
| perfusionregression | Perfusion Regression |
| petSUVR | Compute SUVR from PET time series images |
| plotBasicNetwork | Simple plotBasicNetwork function. |
| 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. |
| randcca | randomized cca function. |
| randsvd | randomized svd function. |
| randwhiten | randomized whitening function. |
| rapidlyInspectImageData | Simple rapidlyInspectImageData function. |
| readNormalizedPopulationData | Read normalized population from h5 file or directory |
| reexports | Objects exported from other packages |
| reflectImage | reflectImage |
| reflectionMatrix | reflectionMatrix |
| regressionNetworkViz | Visualize a regression result by a d3 network visualization. |
| regressProjections | Regression on image set projection |
| regularizeSimlr | Automatically produce regularization matrices for simlr |
| reho | REHO |
| renderImageLabels | 3D surface-based rendering of image segmentation labels |
| renderSurfaceFunction | 3D surface-based rendering of volume images. |
| renormalizeProbabilityImages | Normalize (modified) probability images |
| reorientImage | reorient image by its principal axis |
| resels | Estimates image resels |
| rfSegmentation | A rfSegmentation function. |
| rfSegmentationPredict | A rfSegmentationPredict function. |
| rftPval | RFT p-values |
| rftResults | RFT Statistical Results |
| robustMatrixTransform | Simple robustMatrixTransform function. |
| rsfDenoise | WIP: data-driven denoising for resting state fMRI |
| save.ANTsR | Save R sessions including ANTsR objects |
| segmentationRefinement.predict | Segmentation refinement using corrective learning... |
| segmentationRefinement.train | Segmentation refinement using corrective learning (training) |
| segmentShapeFromImage | convolution-based shape identification |
| simlr | Similarity-driven multiview linear reconstruction model... |
| simlrU | Compute the low-dimensional u matrix for simlr |
| simulateDisplacementField | simulateDisplacementField |
| skeletonize | Skeletonize a binary segmentation. |
| smoothAppGradCCA | cca via sparse smooth matrix prediction |
| 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. |
| 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. |
| taskFMRI | Simple taskFMRI function. |
| temporalwhiten | Simple autocorrelation-based temporal whitening function. |
| testEanat | Test eigenanatomy in order |
| 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). |
| vectorToMultichannel | Convert vector to multichannel 'antsImage'. |
| 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. |
| writeNormalizedPopulationData | Save normalized population data to a directory or h5 file |
