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