Function reference • extrantsr

All functions
`origin()` `origin<-`()	Extract Image Attributes `origin` from `antsImage` or `nifti` objects
`ants.extract()`	Extract values from antsImage from mask
`ants.overlay()`	Plot Lightbox for antsImage
`ants2oro()`	Convert Between antsImage and nifti objects
`antsCopyOrigin()` `antsCopyDirection()` `antsCopySpacing()`	Copy Information of One Image to Another
`ants_apply_transforms()`	Apply ANTs transforms to nifti images
`ants_bwlabel()`	ANTs BWLabel Clusters of Certain Size
`ants_regwrite()`	Registration to a Template
`applyEmptyImageDimensions(<antsImage>)`	Apply Subsetting from Empty Image Dimensions
`apply_malf_regs()`	Apply MALF Registrations
`apply_multi_reg()`	Check if antsImage or read in
`bias_correct()` `bias_correct_ants()`	N3 or N4 Correct
`bias_ss()`	Bias Field Correct then Skull Strip
`brain_extract()`	Wrapper for ANTs brain extraction
`c3d()`	Convert NeuroImage Types
`check_ants(<nifti>)`	Check if antsImage or read in
`check_nifti(<antsImage>)`	Check if nifti image or read in a nifti image
`checkimg(<antsImage>)`	Force object to filename
`compose_transform_to_file()`	Compose Transforms from ANTsR to a composite file
`corr_img()`	Neighborhood Correlation Image
`cort_thickness()` `kk()`	Compute cortical thickness using Kelly Kapowski (ANTsR)
`create_moment()`	Create Neighborhood Momemts of an Image
`diff_self()`	Flipped Difference Image
`double_remove_neck()`	Remove Neck Twice from a Scan
`emptyImageDimensionsMask(<antsImage>)`	Make Mask from Empty Image Dimensions
`face_removal_mask_ants()` `deface_image_ants()`	Face Removal Mask using ANTs Registration
`fill_2d_z()`	Image Mask Filler over each slice in Z-direction
`filler()`	Image Mask Filler
`finite_img(<antsImage>)`	Finite Image
`fslbet_robust()`	Robust Skull Stripping with COG estimation and Bias Correction
`group_xyz2()`	Center of Gravity for Multiple Components/Areas
`image_similarity()`	Compute Image Similarity Metrics
`img_cov_matrix()`	Neighborhood Covariance Matrix
`img_density_entropy()`	Image Entropy using density
`img_hist_entropy()`	Image Entropy using histograms
`img_split()`	Split an Image into Multiple Sub-Images
`inpaint()`	Inpainting of images
`jacobian_image()` `log_jacobian_image()` `geom_jacobian_image()` `log_geom_jacobian_image()`	Image of the Determinant of the Jacobian
`label_clusters()`	Label Clusters
`label_mask()`	Label Connected Components
`largest_component()`	Get Largest Component
`local_quantile_img()`	Quantile Transform Voxel based on Neighborhood Distribution
`makepng()`	Non-exported function to make png
`malf()`	Multi-Atlas Label Fusion
`malf_registration()`	Multi-Atlas Label Fusion Registration
`maskEmptyImageDimensions(<antsImage>)`	Apply Masking from Empty Image Dimensions
`multi_reg()`	Multi-Registration
`multi_rereg()`	Two-Stage Multi-Registration of images
`mutual_information()`	Calculates Mutual Information on nifti objects
`my.tab()`	Quick Tabulation for logical vectors
`n4_4d()`	Four-Dimensional Bias-Field Correction
`neighborhood()`	Get Neighborhood of Voxels from an Image
`neighborhood_index()`	Get Neighborhood Matrix of Indices from an Image
`oMask()` `get_mask()`	Get Mask from nifti object
`oMath()`	Perform iMath on nifti objects
`oasis()`	OASIS Processing Pipeline
`oro2ants()`	Convert Between nifti and antsImage
`ortho2(<antsImage>)` `ortho2(<niftiImage>)`	Orthographic Display, added options
`otropos()`	Run Atropos for nifti objects
`otropos2()`	Run Atropos for nifti objects
`perona_malik()`	Perona-Malik Anisotropic Filter
`pixdim(<antsImage>)`	Extract Image pixdim attribute
`preprocess_mri_across()`	Preprocess MRI acros visits
`preprocess_mri_within()`	Within Visit Registration
`process_filenames()`	Process filenames to ensure nifti and consistency
`read_transformlist()`	Read Transform List from ANTsR
`reapply_malf()`	Reapply MALF Operation
`reg_flip()`	Flip Image with Registration
`reg_flip_img()`	Flip Image with Registration
`reg_whitestripe()`	WhiteStripe Normalization
`reg_zscore()`	Z-score Normalization
`registration()`	Registration Wrapper function
`remove_neck()`	Remove Neck from Image
`reorder_neigh_indices()`	Reorder Voxel Neighborhood
`reproducible_ants()`	Set reproducible seeds and threads for ANTsR execution
`resample_image()` `.resample_image()`	Resample an image
`resample_to_target()` `.resample_to_target()`	Resample an Image to a Target Image
`robust_brain_mask()`	Robust Brain Mask from Template
`scaled_neighborhood()`	Get Scaled Neighborhood of Voxels from an Image
`sim()`	Calculate Overlap Metrics
`smooth_image()`	Gaussian smooth image using ANTsR
`smri_preproc()`	Standard MRI Preprocessing
`ss_bias()`	Skull Strip then Bias Field Correct
`stat_img()`	Create Statistics Image
`subset_4d()` `.subset_4d()`	Subset a 4D image
`tempants()`	Create temporary nii.gz file from antsImage
`transformlist_from_outprefix()`	Get list of transforms that would likely be made with a specific `outprefix`
`within_visit_registration()`	Within Visit Registration
`write_transformlist()`	Read Transform List from ANTsR
`zero_pad()`	Zero pads an image
`zscore_template()`	Create Z-score-to-Template Image

Reference

All functions