| Processing arguments for command line parsing | .int_antsProcessArguments |
| Simple motion_correction function. | .motion_correction |
| Extract or Replace Parts of antsImage Object | [,antsImage,antsImage,ANY,ANY-method [,antsImage,ANY,ANY,ANY-method [,antsImage,ANY,ANY-method [,antsImage,logical,ANY,ANY-method [,antsImage,logical,ANY-method [,antsImage,missing,missing,ANY-method [,antsImage,missing,missing-method [,antsImage,missing,numeric,ANY-method [,antsImage,missing,numeric-method [,antsImage,NULL,ANY,ANY-method [,antsImage,NULL,NULL,ANY-method [,antsImage,NULL,NULL-method [,antsImage,NULL,numeric,ANY-method [,antsImage,NULL,numeric-method [,antsImage,numeric,missing,ANY-method [,antsImage,numeric,missing-method [,antsImage,numeric,NULL,ANY-method [,antsImage,numeric,NULL-method [,antsImage,numeric,numeric,ANY-method [,antsImage,numeric,numeric-method [,ANY,antsImage,ANY,ANY-method [<-,antsImage,antsImage,ANY,ANY-method [<-,antsImage,antsImage-method [<-,antsImage,array,antsRegion,ANY-method [<-,antsImage,array,antsRegion-method [<-,antsImage,array,ANY,ANY-method [<-,antsImage,array-method [<-,antsImage,list,ANY,ANY-method [<-,antsImage,list-method [<-,antsImage,logical,antsRegion,ANY-method [<-,antsImage,logical,antsRegion-method [<-,antsImage,logical,ANY,ANY-method [<-,antsImage,logical-method [<-,antsImage,matrix,antsRegion,ANY-method [<-,antsImage,matrix,antsRegion-method [<-,antsImage,matrix,ANY,ANY-method [<-,antsImage,matrix-method [<-,antsImage,missing,numeric,array-method [<-,antsImage,NULL,antsRegion,ANY-method [<-,antsImage,NULL,antsRegion-method [<-,antsImage,NULL,ANY,ANY-method [<-,antsImage,NULL,NULL,numeric-method [<-,antsImage,NULL,numeric,numeric-method [<-,antsImage,NULL-method [<-,antsImage,numeric,missing,array-method [<-,antsImage,numeric,NULL,numeric-method [<-,antsImage,numeric,numeric,numeric-method |
| Pipe an object forward | %>% |
| AAL Labels | aal |
| An ants-based brain extraction script. | abpBrainExtraction |
| MR image bias correction based on the N4 algorithm. | abpN4 |
| addNoiseToImage | addNoiseToImage |
| Computes the Adjusted RV-Coefficient (Highly Optimized) | adjusted_rvcoef |
| a multi-start optimizer for affine registration | affineInitializer |
| alffmap | alffmap |
| Apply transforms to images. | antsApplyTransforms |
| Apply transforms to points. | antsApplyTransformsToPoints |
| Computes average of image list | antsAverageImages |
| a basic framework for network analysis that produces graph metrics | antsBOLDNetworkAnalysis |
| return ants compile flags | antsCompileFlags |
| Copy header info | antsCopyImageInfo |
| Copy header info with different input order | antsCopyImageInfo2 |
| return ANTs binary directory information | antsDir |
| An S4 class for an antsImage | antsImage-class initialize,antsImage-method show,antsImage-method |
| Math for antsImage Objects | !,antsImage-method abs,antsImage-method acos,antsImage-method acosh,antsImage-method antsImage-math asin,antsImage-method asinh,antsImage-method atan,antsImage-method atanh,antsImage-method ceiling,antsImage-method cos,antsImage-method cosh,antsImage-method cospi,antsImage-method exp,antsImage-method floor,antsImage-method gamma,antsImage-method lgamma,antsImage-method log,antsImage-method log10,antsImage-method log2,antsImage-method Math,antsImage-method round,antsImage-method sign,antsImage-method sin,antsImage-method sinh,antsImage-method sinpi,antsImage-method sqrt,antsImage-method tan,antsImage-method tanh,antsImage-method tanpi,antsImage-method trunc,antsImage-method |
| Operations for antsImage Objects | !=,antsImage,antsImage-method !=,antsImage,ANY-method !=,antsImage,array-method !=,antsImage,list-method !=,ANY,antsImage-method !=,array,antsImage-method %%,antsImage,antsImage-method %%,antsImage,numeric-method %%,numeric,antsImage-method %/%,antsImage,antsImage-method %/%,antsImage,numeric-method %/%,numeric,antsImage-method &,antsImage,antsImage-method &,antsImage,logical-method *,antsImage,antsImage-method *,antsImage,numeric-method *,numeric,antsImage-method +,antsImage,antsImage-method +,antsImage,numeric-method +,numeric,antsImage-method -,antsImage,antsImage-method -,antsImage,numeric-method -,numeric,antsImage-method /,antsImage,antsImage-method /,antsImage,numeric-method /,numeric,antsImage-method <,antsImage,antsImage-method <,antsImage,ANY-method <,antsImage,array-method <,antsImage,list-method <,ANY,antsImage-method <,array,antsImage-method <=,antsImage,antsImage-method <=,antsImage,ANY-method <=,antsImage,array-method <=,antsImage,list-method <=,ANY,antsImage-method <=,array,antsImage-method ==,antsImage,antsImage-method ==,antsImage,ANY-method ==,antsImage,array-method ==,antsImage,list-method ==,ANY,antsImage-method ==,array,antsImage-method >,antsImage,antsImage-method >,antsImage,ANY-method >,antsImage,array-method >,antsImage,list-method >,ANY,antsImage-method >,array,antsImage-method >=,antsImage,antsImage-method >=,antsImage,ANY-method >=,antsImage,array-method >=,antsImage,list-method >=,ANY,antsImage-method >=,array,antsImage-method antsImage-operators anyNA,antsImage-method Arith,antsImage,antsImage-method Arith,antsImage,array-method Arith,antsImage,list-method Arith,antsImage,logical-method Arith,antsImage,missing-method Arith,antsImage,numeric-method Arith,array,antsImage-method Arith,list,antsImage-method Arith,logical,antsImage-method Arith,numeric,antsImage-method is.finite,antsImage-method is.infinite,antsImage-method is.na,antsImage-method is.nan,antsImage-method Logic,antsImage,antsImage-method Logic,antsImage,ANY-method Logic,antsImage,array-method Logic,antsImage,list-method Logic,antsImage,logical-method Logic,antsImage,numeric-method Logic,ANY,antsImage-method Logic,array,antsImage-method Logic,list,antsImage-method Logic,logical,antsImage-method Logic,numeric,antsImage-method which,antsImage-method ^,antsImage,antsImage-method ^,antsImage,numeric-method ^,numeric,antsImage-method |,antsImage,antsImage-method |,antsImage,logical-method |
| Summary for antsImage Objects | all antsImage-summary any max max,antsImage-method min min,antsImage-method prod range sum Summary,antsImage-method |
| Clone an 'antsImage'. | antsImageClone |
| antsImageGetSet | antsGetDirection antsGetOrigin antsGetSpacing antsImageGetSet antsSetDirection antsSetOrigin antsSetSpacing |
| Read file info from image header | antsImageHeaderInfo |
| antsImageIterator | antsImageIterator |
| An S4 class for an antsImageIterator | antsImageIterator-class initialize,antsImageIterator-method show,antsImageIterator-method |
| antsImageIteratorGet | antsImageIteratorGet |
| antsImageIteratorGetIndex | antsImageIteratorGetIndex |
| antsImageIteratorGoToBegin | antsImageIteratorGoToBegin |
| antsImageIteratorGoToReverseBegin | antsImageIteratorGoToReverseBegin |
| antsImageIteratorIsAtEnd | antsImageIteratorIsAtEnd |
| antsImageIteratorIsAtReverseEnd | antsImageIteratorIsAtReverseEnd |
| antsImageIteratorNext | antsImageIteratorNext |
| antsImageIteratorPrevious | antsImageIteratorPrevious |
| antsImageIteratorRemaining | antsImageIteratorRemaining |
| antsImageIteratorSet | antsImageIteratorSet |
| antsImageIteratorSetIndex | antsImageIteratorSetIndex |
| mutual information between two images | antsImageMutualInformation |
| Check for physical space consistency | antsImagePhysicalSpaceConsistency |
| Image Read | antsImageRead |
| Cast images to either a passed pixeltype or the most precise of the inputs | antsImageTypeCast |
| Image Write | antsImageWrite |
| return ANTs installation information | antsIncludes |
| return ants library location | antsLibs |
| antsMatrix Class | antsMatrix-class initialize,antsMatrix-method |
| antsMotionCalculation | antsMotionCalculation |
| Motion Correction | antsMotionCorr |
| return nuisance variable strings | antspymm_nuisance_names |
| Generate Predictors from ANTsPyMM Imaging Data | antspymm_predictors |
| Get Quality Control (QC) Metric Names | antspymm_qc_names |
| Determine the Variable Type Based on Its Name | antspymm_vartype |
| Generate Multi-view CCA-based Feature Projections for a List of Matrices | antsr_mcca_features |
| Generate PCA-based feature projections for a list of voxel matrices | antsr_pca_features |
| Generate reproducible random feature projections for a list of voxel matrices | antsr_random_features |
| Multi-view Regularized CCA baseline using RGCCA | antsr_rgcca_baseline |
| Sparse Multi-view CCA Baseline using RGCCA (version-safe) | antsr_rgcca_sparse |
| Generate sparse PCA-based feature projections for a list of voxel matrices | antsr_spca_features |
| An S4 class to hold a region of an antsImage | antsRegion-class |
| Perform registration between two images. | antsRegistration |
| Return the antsImage pointer string | antsrGetPointerName |
| antsrimpute | antsrimpute |
| An S4 class for image metrics between two antsImages | antsrMetric-class initialize,antsrMetric-method show,antsrMetric-method |
| 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 |
| Render a function onto a surface. | antsrSurf |
| An S4 class for an antsrTransform | antsrTransform-class initialize,antsrTransform-method show,antsrTransform-method |
| antsrTransformFromDisplacementField | antsrTransformFromDisplacementField |
| antsrVersions | antsrVersions |
| Render an image volume with or without overlay. | antsrVol |
| Set a pixel value at an index | antsSetPixels |
| Perform spatial ICA on fMRI bold data. | antsSpatialICAfMRI |
| Get Spatial Point from Index | antsTransformIndexToPhysicalPoint |
| Get Index from Spatial Point | antsTransformPhysicalPointToIndex |
| antsVersions | antsVersions |
| Extension of apply to allow input of antsImage | apply apply.antsImage apply.default |
| Apply SIMLR projection matrices with r01.1-style versioning | apply_simlr_matrices |
| Apply simlr matrices to an existing data frame and combine the results with DTI naming fix. | apply_simlr_matrices_dtfix |
| Apply a learned transform to a new matrix | apply_transform_matrix |
| applyAntsrTransform | applyAntsrTransform |
| applyAntsrTransformToImage | applyAntsrTransformToImage |
| applyAntsrTransformToPoint | applyAntsrTransformToPoint |
| applyAntsrTransformToVector | applyAntsrTransformToVector |
| Convert Objects into antsImage objects | as.antsImage as.antsImage,array-method as.antsImage,matrix-method |
| Coerce Object to as.antsMatrix | as.antsMatrix as.antsMatrix,data.frame-method as.antsMatrix,list-method as.antsMatrix,matrix-method |
| Coerce antsImage objects to array | as.array as.array,antsImage-method as.array.antsImage as.character.antsImage as.data.frame,antsMatrix-method as.data.frame.antsMatrix as.factor.antsImage as.list,antsMatrix-method as.matrix,antsImage-method as.matrix,antsMatrix-method as.matrix.antsImage as.numeric,antsImage-method dim,antsImage-method factor.antsImage |
| Average ASL tag-control pairs to estimate perfusion | aslAveraging |
| Censor bad volumes from ASL data. | aslCensoring |
| WIP: data-driven denoising for ASL MRI | aslDenoiseR |
| ASL-based Perfusion from PASL, CASL or pCASL. | aslPerfusion |
| FMM Segmentation | atropos |
| Robust SVD with Automatic rsvd Fallback | ba_svd |
| backup simlr implementation | backup_simlr |
| basal_forebrain | basal_forebrain |
| Inpaints missing imaging data from boundary data | basicInPaint |
| Uses probabilistic segmentation to constrain pcasl-based cbf computation. | bayesianCBF |
| Simple bayesian regression function. | bayesianlm |
| Efficiently compute basic statistical inference from regressions with multiple outcomes | bigLMStats |
| Block stimulus model for FMRI Data | blockStimulus |
| Calculate blood perfusion using deconvolution. | bloodPerfusionSVD |
| BOLD Correlation Matrix | bold_correlation_matrix |
| Boxplot of Values in an Image | boxplot.antsImage |
| ANTs template building. | buildTemplate |
| Calculate SiMLR energy for optimization | calculate_simlr_energy |
| Calculate SiMLR Similarity Gradient | calculate_simlr_gradient |
| cerebellum | cerebellum |
| cerebellum_labels | cerebellum_labels |
| Check if antsImage or read in | check_ants check_ants,antsImage-method check_ants,ANY-method check_ants,character-method check_ants,list-method check_ants-methods |
| Check a matrix for zero-variance rows and columns | check_zero_variance |
| cit168_brainstem | cit168_brainstem |
| cit168_reinf_learn | cit168_reinf_learn |
| CIT168 reinforcement learning atlas label descriptions | CIT168_Reinf_Learn_v1_label_descriptions_pad |
| CIT168 T1w 700um pad adni brainstem | CIT168_T1w_700um_pad_adni_brainstem |
| Clip a Gradient Matrix by a Quantile of its Values | clip_gradient_by_quantile |
| Clip a Gradient Matrix by its Frobenius Norm | clip_gradient_norm |
| Split time series image into k distinct images | clusterTimeSeries |
| Simple Mask Maker | coerce_mask |
| Combine and reduce dimensionality of nuisance predictors. | combineNuisancePredictors |
| Compcors the input matrix using SVD and returns the result. | compcor |
| composeAntsrTransforms | composeAntsrTransforms |
| composeDisplacementFields | composeDisplacementFields |
| Compose arbitrary transform list into a deformation field. | composeTransformsToField |
| Compute Communalities from Factor Scores | compute_communalities |
| Compute Variance Explained per Factor | compute_variance_explained_per_factor |
| computeDVARS | computeDVARS |
| computeDVARSspatialMap | computeDVARSspatialMap |
| Construct SiMLR Feature Names | construct_sim_names |
| convolve one image with another | convolveImage |
| produces a correlation matrix via weighted correlation. | corw |
| Create and Initialize a SIMLR Optimizer | create_optimizer |
| createAntsrTransform | createAntsrTransform |
| createJacobianDeterminantImage | createJacobianDeterminantImage |
| Create a warped grid for visualization. | createWarpedGrid |
| crop a sub-image via a mask | cropImage |
| Crop the center of an image. | cropImageCenter |
| Crop a patch from an image around a center point | cropImageFromCenterPoint |
| crop a sub-image by image indices | cropIndices |
| Cross-Validated R^2 value | crossvalidatedR2 |
| Perform Cut on an image | cut.antsImage |
| Cross-validation method for eigenanatomy decompositions. | cvEigenanatomy |
| Randomly transform image data. | dataAugmentation |
| Decode ANTsPyMM technical shorthand to legible anatomical names | decode_pymm_names |
| Regularize SVD (deconvolution) solution of cerebral blood flow. | deconvolutionSVD |
| decrop a sub-image back into the full image | decropImage |
| Denoise an image | denoiseImage |
| Density of Values in an Image | density.antsImage |
| DesikanKillianyTourville | DesikanKillianyTourville |
| Compute pairwise Dice overlaps for matrix rows or columns | dice_overlap_soft_matrix |
| Compute Dice overlap for sparse vectors with optional quantile thresholding | dice_overlap_soft_vector |
| displacementFieldFromAntsrTransform | displacementFieldFromAntsrTransform |
| Divide each column by the sum of column absolute values | divide_by_column_sum |
| dkt | dkt |
| dkt_cit_labels | dkt_cit_labels |
| dkt cortex cit deep brain | dkt_cortex_cit_deep_brain |
| dkt_labels | dkt_labels |
| dlbs | dlbs |
| Eigenanatomy with deflation | eanatDef |
| Selection of n eigenvectors and sparsity for eigenanatomy | eanatSelect |
| Segmentation for eigenanatomy. | eigSeg |
| Create a Smoothed Sparse Matrix via Permutation Ensemble Averaging | ensembled_sparsity |
| Stop if not an antsImage object | error_not_antsImage |
| Estimate the Joint Rank of a Multi-View Dataset via Parallel Analysis | estimate_joint_rank |
| Estimate Robust Learning Rate for NSA-Flow | estimate_learning_rate_nsa |
| Estimate Joint Rank via Cross-View RV Analysis | estimate_rank_by_permutation_rv |
| Estimate image smoothness | estSmooth |
| Euler Character | euler |
| Uses example images to inpaint or approximate an existing image. | exemplarInpainting |
| Exploratory Clustering and Visualization | exploratory_visualization |
| Extend an existing SIMLR embedding with new modality blocks | extend_simlr_embedding_with_new_modalities |
| Extract 2-D or 3-D image patch coordinates. | extractImagePatchCoordinates |
| Extract 2-D or 3-D image patches. | extractImagePatches |
| extract a slice from an image | extractSlice |
| FA JHU labels edited | FA_JHU_labels_edited |
| Fast Matrix Whitening | fast_whiten |
| Fast Marching Extension filter will extend an intensity or label image from a known region into the unknown region along a geodesic path | fastMarchingExtension |
| Basic pre-processing for BOLD or ASL-based network analysis. | filterfMRIforNetworkAnalysis |
| fitBsplineDisplacementField | fitBsplineDisplacementField |
| fitBsplineObjectToScatteredData | fitBsplineObjectToScatteredData |
| fitThinPlateSplineDisplacementField | fitThinPlateSplineDisplacementField |
| fitTimeVaryingTransformToPointSets | fitTimeVaryingTransformToPointSets |
| fitTransformToPairedPoints | fitTransformToPairedPoints |
| Multi-run normalization, filtering and nuisance estimation for fMRI. | fMRINormalization |
| Band pass filtering for BOLD image. | frequencyFilterfMRI |
| Frobenius Norm of a Matrix | frob |
| fsl2antsrTransform | fsl2antsrTransform |
| Ventilation-based segmentation of hyperpolarized gas lung MRI. | functionalLungSegmentation |
| Manifold-Regularized Fused Ridge Regression | fusedRidge |
| Direct Manifold-Regularized Fused Ridge Regression (General) | fusedRidgeDirect |
| PyTorch-Based Manifold-Regularized Fused Ridge Regression | fusedRidgeTorch |
| fuzzySpatialCMeansSegmentation | fuzzySpatialCMeansSegmentation |
| Generate a Sophisticated Simulated Multi-View Dataset | generate_structured_multiview_data |
| Automatically generate an arterial input function mask. | generateAifMaskImage |
| brain segmentation based on geometric priors | geoSeg |
| getANTsRData | getANTsRData |
| getAntsrTransformFixedParameters | getAntsrTransformFixedParameters |
| getAntsrTransformParameters | getAntsrTransformParameters |
| Get nuisance predictors from ASL images | getASLNoisePredictors |
| getAverageOfTimeSeries | getAverageOfTimeSeries |
| center of mass | getCenterOfMass |
| Convert an image to the geometric centroids of its signal | getCentroids |
| Extract generic fMRI nuisance variables for ASL or BOLD | getfMRInuisanceVariables |
| Get Mask | getMask |
| build multiple resolution predictor matrix from feature images | getMultiResFeatureMatrix |
| Label multivariate components by an anatomical coordinate system. | getMultivariateTemplateCoordinates |
| Extract column names with concatenated search parameters | getNamesFromDataframe |
| Get a hypercube neighborhood at a voxel | getNeighborhoodAtVoxel |
| Get neighborhoods for voxels within mask | getNeighborhoodInMask |
| Get Pixels | getPixels |
| Define an anatomical coordinate system in a new image based on a template | getTemplateCoordinates |
| Impute missing data using GLM models | glm_impute |
| Compute the Gradient of the Orthogonality Defect | gradient_invariant_orthogonality_defect |
| Gradient of the Invariant Orthogonality Defect Measure | gradient_invariant_orthogonality_salad |
| hausdorffDistance | hausdorffDistance |
| hemisphere | hemisphere |
| Linear Model for FMRI Data | hemodynamicRF |
| hessianObjectness | hessianObjectness |
| Histogram of Values in an Image | hist.antsImage |
| histogramEqualizeImage | histogramEqualizeImage |
| histogramMatchImage | histogramMatchImage |
| Transform image intensities based on histogram mapping. | histogramMatchImage2 |
| Transform image intensities based on histogram mapping. | histogramWarpImageIntensities |
| Humanize anatomical names by expanding abbreviations and reordering | humanize_anatomical_name |
| iBind | iBind |
| Simple icawhitening function. | icawhiten |
| Efficiently compute an image-based linear regression model (ilr) | ilr |
| Predict from ilr output | ilr.predict |
| Converts an image to several independent images. | image2ClusterImages |
| Image domain to spatial position | imageDomainToSpatialMatrix |
| Simple imageFileNames2ImageListing function. | imageFileNames2ImageList |
| Read Images into a Matrix | imageListToMatrix |
| imageSimilarity | imageSimilarity |
| Read Images into a Matrix | imagesToMatrix |
| iMath | iMath |
| Operations for iMath Operator | iMathOps |
| Helper Function to Optimize Indicator Matrix with Best Sum | indicator_opt_both_ways |
| Convert a matrix to a form that can be used to initialize sparse cca and pca. | initializeEigenanatomy |
| Initialize simlr | initializeSimlr |
| Integrate vector field | integrateVectorField |
| integrateVelocityField | integrateVelocityField |
| Simple interleaveMatrixWithItself function. | interleaveMatrixWithItself |
| Interpret SiMLR Vector | interpret_simlr_vector |
| Interpret SiMLR Vector | interpret_simlr_vector2 |
| Inverse Square Root of a Symmetric Matrix | inv_sqrt_sym |
| Inverse square root of a symmetric matrix via Newton-Schulz | inv_sqrt_sym_newton |
| Calculate the invariant orthogonality defect | invariant_orthogonality_defect |
| invertAntsrTransform | invertAntsrTransform |
| invertDisplacementField | invertDisplacementField |
| is.antsImage | is.antsImage |
| jhu_fa_labels | jhu_fa_labels |
| jhu_md_labels | jhu_md_labels |
| Propagate Joint Label Fusion (JLF) solutions through a time series | jlfProp |
| Simple joinEigenanatomy function. | joinEigenanatomy |
| joint label and intensity fusion | jointLabelFusion |
| joint smooth matrix prediction | jointSmoothMatrixReconstruction |
| Compute cortical thickness using the DiReCT algorithm. | kellyKapowski |
| k means image segmentation. | kmeansSegmentation |
| k-nearest neighbors constrained image smoothing | knnSmoothImage |
| k-nearest neighbors constrained smoothing | knnSmoothingMatrix |
| L1 Normalize Columns of a Matrix | l1_normalize_features |
| Simple labelClustering function. | labelClusters |
| labelGeometryMeasures | labelGeometryMeasures |
| labelImageCentroids | labelImageCentroids |
| Perform label image registration. | labelImageRegistration |
| labelOverlapMeasures | labelOverlapMeasures |
| Convert label image to a matrix | labels2matrix |
| labelStats | labelStats |
| Simple list append tool | lappend |
| List Available SIMLR Optimizers | list_simlr_optimizers |
| Load R sessions with ANTsR objects | load.ANTsR |
| lobes | lobes |
| lobes_brainstem | lobes_brainstem |
| Local gyrification index. | localGyrificationIndex |
| local joint label and intensity fusion | localJointLabelFusion |
| Produces a low rank version of the input matrix | lowrankRowMatrix |
| Rotate an existing 3d window into different views. | make3ViewPNG |
| Simple function to create and measure a graph from a square input matrix. | makeGraph |
| Simple makeImage function. | makeImage |
| Create label image from physical space points | makePointsImage |
| Label image from Powers points | makePowersPointsImage |
| Convert left/right variables to a measure of asymmetry | mapAsymVar |
| Convert left/right variables to an average measurement | mapLRAverageVar |
| Simple Value extractor for antsImage Values | mask_values |
| Mask input image by mask image. | maskImage |
| Simple matrix2timeseries function. | matrix2timeseries |
| Convert rows of a matrix to images | matrixToImages |
| MD JHU labels edited | MD_JHU_labels_edited |
| Mean for antsImage Objects | mean.antsImage |
| Median for antsImage Objects | median.antsImage |
| merge images into a multiChannel antsImage | mergeChannels |
| mergeListToNDImage | mergeListToNDImage |
| Efficiently compute a multivariate, image-based (mixed) linear decompositition (mild) | mild |
| Efficiently compute a multivariate, penalized image-based linear regression model (milr) | milr |
| Predict from a milr output | milr.predict |
| Brett's mni2tal | mni2tal |
| Morphological image operations | morphology |
| multi-res voxelwise neighborhood random forest segmentation learning | mrvnrfs |
| multi-res voxelwise neighborhood random forest segmentation | mrvnrfs.predict |
| mtl description | mtl_description |
| mtl_labels | mtl_labels |
| Shape analysis of multichannel images based on PCA | multichannelPCA |
| Convert multichannel 'antsImage' to a vector. | multichannelToVector |
| Grep entries with a vector search parameters | multigrep |
| Morphology on multi label images. | multiLabelMorphology |
| multiple resolution neighborhood random forest regression | multiResRandomForestRegression |
| Multi-scale svd | multiscaleSVD |
| Multiview PCA | multiview_pca |
| N3 bias field correction | n3BiasFieldCorrection |
| N3 Bias field correction | n3BiasFieldCorrection2 |
| N4 bias field correction | n4BiasFieldCorrection |
| nbm3_labels | nbm3_labels |
| nbm3CH13 | nbm3CH13 |
| Nonnegativity Violation | neg_violation |
| Convenience wrapper for eigenanatomy decomposition. | networkEiganat |
| Perform SiMLR Analysis on Multimodal ANTsPyMM Data | NNHEmbed |
| Update Residuals for SiMLR | NNHEmbed_update_residuals |
| NSA-Flow Optimization | nsa_flow |
| NSA-Flow Optimization via PyTorch AutoGrad (R wrapper) | nsa_flow_autograd |
| Generate NSA-Flow FA Flowchart Diagram | nsa_flow_fa_diagram |
| NSA-Flow Algorithm Flowchart | nsa_flow_flowchart |
| NSA-Flow Sparse PCA (stable + efficient) | nsa_flow_pca |
| NSA-Flow Sparse PCA or FA | nsa_flow_pca_fa |
| Perform Proximal Gradient Optimization for PCA or Factor Analysis | nsa_flow_pca_fa_2 |
| Retraction onto the Stiefel Manifold | nsa_flow_retract |
| Retraction onto the Stiefel Manifold (soft-polar multiplicative, with adaptive inv-sqrt) | nsa_flow_retract_auto |
| NSA-Flow Optimization via PyTorch | nsa_flow_torch |
| NSA-Flow Optimization via PyTorch AutoGrad | nsa_flow_torch_ag |
| Inverse one-hot transformation | oneHotToSegmentation |
| Calculate SiMLR energy for optimization Find Optimal SiMLR Initializer | optimal_simlr_initializer |
| Optimize Binary Indicator Matrix with Row Uniformity | optimize_indicator_matrix |
| Orthogonality Residual | orth_residual |
| Orthogonalize a List of Matrices via Gradient Descent with Convergence Check | orthogonalize_feature_space |
| Sparsify and optionally orthogonalize a matrix | orthogonalizeAndQSparsify |
| sparsify a matrix | orthogonalizeAndQSparsifyOld |
| Pad an image based on a factor. | padImageByFactor |
| Pad or crop image to a specified size | padOrCropImageToSize |
| pairwise application of matrix similarity to matrix List projected onto a feature list | pairwise_matrix_similarity |
| Simple pairwiseImageDistanceMatrix function for images | pairwiseImageDistanceMatrix |
| Perform partial volume correction for ASL images. | partialVolumeCorrection |
| Perfusion Regression | perfusionregression |
| Compute SUVR from PET time series images | petSUVR |
| Extract Image Attributes 'pixeltype' from antsImages | components components,antsImage-method components<- components<-,antsImage-method direction direction,antsImage-method direction<- direction<-,antsImage-method origin origin,antsImage-method origin<- origin<-,antsImage-method pixeltype pixeltype,antsImage-method pixeltype<- pixeltype<-,antsImage-method spacing spacing,antsImage-method spacing<- spacing<-,antsImage-method |
| Plot Energy Decomposition During SIMLR Optimization | plot_energy_decomposition |
| Plot Features | plot_features |
| Plotting an image slice or multi-slice with optional color overlay. | plot.antsImage |
| Simple plotBasicNetwork function. | plotBasicNetwork |
| Simple plotPrettyGraph function saves to png. | plotPrettyGraph |
| Post-hoc Factor Analysis Summary: Scores, Communalities, and Variance Explained | posthoc_fa_summary |
| powers_areal_mni_itk | powers_areal_mni_itk |
| powers mni itk | powers_mni_itk |
| ppmi template 500Parcels Yeo2011 17Networks 2023 homotopic | ppmi_template_500Parcels_Yeo2011_17Networks_2023_homotopic |
| ppmi_yeo_labels | ppmi_yeo_labels |
| Predict Method for Fused Ridge Regression | predict.fusedRidge |
| Predict Method for Direct Fused Ridge Regression | predict.fusedRidgeDirect |
| Predict Method for PyTorch Fused Ridge Regression | predict.fusedRidgeTorch |
| predict output matrices from simlr solution | predictSimlr |
| Preprocess BOLD fMRI image data. | preprocessfMRI |
| Preprocess resting BOLD fMRI image data. | preprocessRestingBOLD |
| spatial prior-based image segmentation. | priorBasedSegmentation |
| Project Non-Negative Matrix to Orthonormal Columns Matrix | project_to_orthonormal_nonnegative |
| Project Non-Negative Matrix with Controllable Orthonormality | project_to_partially_orthonormal_nonnegative |
| quantifyCBF | quantifyCBF |
| Simple quantifySNPs function. | quantifySNPs |
| Sample Quantiles | quantile.antsImage |
| randomized cca function. | randcca |
| Randomly transform image data (optional: with corresponding segmentations). | randomlyTransformImageData |
| Get a random mask | randomMask |
| randomized svd function. | randsvd |
| randomized whitening function. | randwhiten |
| rank-based segmentation of a matrix | rankBasedMatrixSegmentation |
| rank intensity transformation for an image | rankIntensity |
| Simple rapidlyInspectImageData function. | rapidlyInspectImageData |
| Read all SiMLR outputs from disk | read_simlr |
| Read a list of data frames from disk with SiMLR-specific naming convention | read_simlr_data_frames |
| readAntsrTransform | readAntsrTransform |
| Read normalized population from h5 file or directory | readNormalizedPopulationData |
| Reconstruct image from a list of patches. | reconstructImageFromPatches |
| refbasis brain | refbasis_brain |
| refbasis head | refbasis_head |
| reference basis | reference_basis |
| reflectImage | reflectImage |
| reflectionMatrix | reflectionMatrix |
| Image intensity normalization using linear regression. | regressionMatchImage |
| Regression on image set projection | regressProjections |
| Automatically produce regularization matrices for simlr | regularizeSimlr |
| REHO | reho |
| Normalize (modified) probability images | renormalizeProbabilityImages |
| reorient image by its principal axis | reorientImage |
| resampleImage | resampleImage |
| resampleImageToTarget | resampleImageToTarget |
| Estimates image resels | resels |
| Reset Optimizer State | reset_optimizer_state |
| A rfSegmentation function. | rfSegmentation |
| A rfSegmentationPredict function. | rfSegmentationPredict |
| RFT p-values | rftPval |
| RFT Statistical Results | rftResults |
| Minimal function for creating r images | ri |
| Rotation Invariant Patch-based Multi-Modality Analysis aRChitecture | ripmmarc |
| Generate an antsImage from ripmmarc basis data | ripmmarcBasisImage |
| RIPMMARC population basis | ripmmarcPop |
| Simple robustMatrixTransform function. | robustMatrixTransform |
| WIP: data-driven denoising for resting state fMRI | rsfDenoise |
| Computes the RV-Coefficient (Optimized Public API) | rvcoef |
| Computes the RV-Coefficient (Internal) | rvcoef_components |
| Computes the RV-Coefficient (Internal) Gram Matrix Method for Tall data | rvcoef_gram_impl |
| Computes the RV-Coefficient (Internal) Trace Method for Wide data | rvcoef_trace_impl |
| Safe PCA with Deterministic Bad-Column Repair | safe_pca |
| Save R sessions including ANTsR objects | save.ANTsR |
| Scale space feature detector | scaleSpaceFeatureDetection |
| SD generic | sd sd.antsImage sd.default |
| Segmentation refinement using corrective learning (prediction) | segmentationRefinement.predict |
| Segmentation refinement using corrective learning (training) | segmentationRefinement.train |
| One-hot encoding function | segmentationToOneHot |
| convolution-based shape identification | segmentShapeFromImage |
| Select an Optimal Joint Number of Components for Multi-View Data | select_joint_k |
| Set ANTs deterministic behavior | setANTsDeterministic |
| setAntsrTransformFixedParameters | setAntsrTransformFixedParameters |
| setAntsrTransformParameters | setAntsrTransformParameters |
| Set Seed Based on Current Time | setSeedBasedOnTime |
| shorter antspymm names | shorten_pymm_names |
| Similarity-driven multiview linear reconstruction model (simlr) for N modalities | simlr |
| Compute the Average Invariant Orthogonality Defect for Multiple Features | simlr_feature_orth |
| Impute missing SiMLR data in a specified column based on other columns | simlr_impute |
| SiMLR Path Models helper | simlr_path_models |
| Apply SIMLR Sparseness and Normalize Features | simlr_sparseness |
| Generate Parameter Grid for SIMLR Search | simlr.parameters |
| Assess Significance of SiMLR Call | simlr.perm |
| Perform Parallel SIMLR Grid Search (with Progress Bar) | simlr.search |
| Compute the low-dimensional u matrix for simlr | simlrU |
| Simulate random bias field | simulateBiasField |
| simulateDisplacementField | simulateDisplacementField |
| Skeletonize a binary segmentation. | skeletonize |
| cca via sparse smooth matrix prediction | smoothAppGradCCA |
| Smooth image | smoothImage |
| smooth matrix prediction | smoothMatrixPrediction |
| Reconstruct a n by k vector given n by p matrix of predictors. | smoothMultiRegression |
| smooth matrix-based regression | smoothRegression |
| softwareVersions | softwareVersions |
| Convenience wrapper for eigenanatomy decomposition. | sparseDecom |
| Convenience wrapper for 2-view eigenanatomy decomposition. | sparseDecom2 |
| Convenience wrapper for 2-view eigenanatomy decomposition w/bootstrap initialization. | sparseDecom2boot |
| Convenience wrapper for eigenanatomy decomposition. | sparseDecomboot |
| Create sparse distance, covariance or correlation matrix | sparseDistanceMatrix |
| Create sparse distance, covariance or correlation matrix from x, y | sparseDistanceMatrixXY |
| Sparse regression on input images. | sparseRegression |
| Sparsify a Matrix via Column-wise Winner-Take-All | sparsify_by_column_winner |
| spatially constrained bayesian regression function. | spatialbayesianlm |
| split a multichannel antsImage | splitChannels |
| Split data for testing and training | splitData |
| split a mask into n labeled sub-masks | splitMask |
| splitNDImageToList | splitNDImageToList |
| Produces a threshold value based on cluster or voxel level statistics | statFieldThresh |
| Take One Optimization Step | step |
| Simple subgradientL1Regression function. | subgradientL1Regression |
| convert subject matrix data to a row in a dataframe. | subjectDataToGroupDataFrame |
| Subsetting antsImage Objects | subset.antsImage |
| Sum preserving matrix partition | sum_preserving_matrix_partition |
| Symmetrize a Matrix | symm |
| T template0 LobesBstem | T_template0_LobesBstem |
| Take Absolute Value of Unsigned Columns | take_abs_unsigned |
| Simple taskFMRI function. | taskFMRI |
| Simple autocorrelation-based temporal whitening function. | temporalwhiten |
| Test eigenanatomy in order | testEanat |
| Threshold Image | thresholdImage |
| Time-series image to matrix | timeseries2matrix |
| Run N3 on slices of timeseries. | timeseriesN3 |
| Time-series image to matrix of time windows around user-specified events | timeserieswindow2matrix |
| tissues | tissues |
| tracts | tracts |
| Transform a matrix by standard preprocessing | transform_matrix |
| Transform prior rows to (approximately) uncorrelated representative rows | transform_prior_rows_to_uncorrelated |
| Calculate the area under a sampled curve (or set of curves). | trapz |
| Undo a previously applied matrix transform | undo_transform_matrix |
| Unique for antsImage Objects | unique.antsImage |
| Use any package. If package is not installed, this will install from CRAN. | usePkg |
| Variance generic | var var.antsImage var.default |
| Convert a Vector to a Data Frame | vector_to_df |
| Convert vector to multichannel 'antsImage'. | vectorToMultichannel |
| Visualize Low-Rank Relationships | visualize_lowrank_relationships |
| Visualize Permutation Test Results | visualize_permutation_test |
| voxelwise neighborhood random forest segmentation and prediction | vwnrfs |
| voxelwise neighborhood random forest prediction | vwnrfs.predict |
| image curvature for 2D or 3D | weingartenImageCurvature |
| Simple whitening function. | whiten |
| Whitening Matrix | whiten_matrix |
| wm_major_tracts | wm_major_tracts |
| wmh_evidence | wmh_evidence |
| Write all SiMLR outputs to disk | write_simlr |
| Write a list of data frames to disk with SiMLR-specific naming convention | write_simlr_data_frames |
| writeAntsrTransform | writeAntsrTransform |
| Save normalized population data to a directory or h5 file | writeNormalizedPopulationData |
