Package: rpyANTs 0.0.3.9005

rpyANTs: An Alternative Advanced Normalization Tools ('ANTs')

Provides portable access from 'R' to biomedical image processing toolbox 'ANTs' by Avants et al. (2009) <doi:10.54294/uvnhin> via seamless integration with the 'Python' implementation 'ANTsPy'. Allows biomedical images to be processed in 'Python' and analyzed in 'R', and vice versa via shared memory. See 'citation("rpyANTs")' for more reference information.

Authors:Zhengjia Wang [aut, cre]

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NEWS

# Install 'rpyANTs' in R:

install.packages('rpyANTs', repos = c('https://dipterix.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dipterix/rpyants/issues

On CRAN:

ants brain ieeg mri neuroimaging normalization python registration

52 exports 1 stars 1.26 score 33 dependencies 206 downloads

Last updated 2 days agofrom:0d1244e4ef

Exports:ants ants_apply_transforms ants_apply_transforms_to_points ants_available ants_motion_correction ants_plot ants_plot_grid ants_registration ants_resample_image antspynet_brain_extraction antspynet_deep_atropos antspynet_desikan_killiany_tourville_labeling antspynet_preprocess_brain_image as_ANTsImage as_ANTsTransform correct_intensity ensure_template halpern_apply_transform_template_mri halpern_register_ct_mri halpern_register_template_mri import install_ants is_affine3D load_ants load_antspynet np_array py py_bool py_builtin py_call py_del_attr py_del_item py_dict py_eval py_get_attr py_get_item py_help py_len py_list py_none py_run_string py_set_attr py_set_item py_slice py_str py_to_r py_to_r_wrapper r_to_py repl_python run_script t1_preprocess tuple

Dependencies:base64enc cli crayon digest evaluate fansi fastmap glue here htmltools IRdisplay IRkernel jsonlite lattice lifecycle Matrix pbdZMQ pillar png rappdirs Rcpp RcppTOML repr reticulate rlang RNifti rprojroot rpymat rstudioapi utf8 uuid vctrs withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get 'ANTsPy' module	ants load_ants
Apply a transform list to map an image from one domain to another	ants_apply_transforms
Apply a transform list to map points from one domain to another	ants_apply_transforms_to_points
Check if 'ANTs' is available	ants_available
Motion correction	ants_motion_correction
Plot single ''ANTsImage''	ants_plot
Plot multiple ''ANTsImage''	ants_plot_grid
Register two images using 'ANTs'	ants_registration
Resample image	ants_resample_image
Get ''ANTsPyNet'' module	antspynet load_antspynet
Extract brain and strip skull	antspynet_brain_extraction
Process brain image prior to segmentation	antspynet_preprocess_brain_image
Imaging segmentation using 'antspynet'	antspynet_deep_atropos antspynet_desikan_killiany_tourville_labeling antspynet_segmentation
Load data as ''ANTsImage'' class	as_ANTsImage
Convert to ''ANTsTransform''	as_ANTsTransform as_ANTsTransform.ants.core.ants_image.ANTsImage as_ANTsTransform.ants.core.ants_transform.ANTsTransform as_ANTsTransform.character as_ANTsTransform.default as_ANTsTransform.numpy.ndarray
Truncate and correct 'MRI' intensity	correct_intensity
Ensure the template directory is downloaded	ensure_template
'ANTs' functions for 'Halpern' lab	halpern_apply_transform_template_mri halpern_preprocess halpern_register_ct_mri halpern_register_template_mri
Install 'ANTs' via 'ANTsPy'	install_ants
Check if an object is a 3D 'affine' transform matrix	is_affine3D is_affine3D.ants.core.ants_transform.ANTsTransform is_affine3D.default
Get 'Python' main process environment	py
Get 'Python' built-in object	py_builtin
List in 'Python'	py_list
Slice index in 'Python' arrays	py_slice
Process 'T1' image	t1_preprocess