https://github.com/antsx/antsr

R interface to the ANTs biomedical image processing library

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
Links to: ncbi.nlm.nih.gov, nature.com
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Committers with academic emails
4 of 25 committers (16.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.4%) to scientific vocabulary

Keywords

brain decomposition mri r registration segmentation

Keywords from Contributors

image-registration medical-image-processing neuroimaging image-analysis insight-toolkit itk medical-imaging numfocus open-science convolutional-neural-networks

Last synced: 5 months ago · JSON representation

Repository

R interface to the ANTs biomedical image processing library

Basic Info

Host: GitHub
Owner: ANTsX
License: apache-2.0
Language: R
Default Branch: master
Homepage: https://antsx.github.io/ANTsR
Size: 62.6 MB

Statistics

Stars: 135
Watchers: 25
Forks: 35
Open Issues: 43
Releases: 29

Topics

brain decomposition mri r registration segmentation

Created over 13 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License Code of conduct

Advanced Normalization Tools in R

Downloads

ANTsR is an R package which wraps the well-established C++ biomedical image processing library ANTs. It includes efficient reading and writing of medical images, algorithms for registration, segmentation, and statistical learning, as well as functions to create publication-ready visualizations.

If you are looking to train deep learning models on your medical images in R, you might be interested in ANTsRNet which provides pre-trained models and utilities for training deep learning models on medical images.

Installation

The ANTsR package can be installed the pre-compiled binaries (fast) or from source. We are actively working on getting ANTsR onto a host like CRAN or BioConductor.

Pre-compiled binaries

The fastest way to install ANTsR is from pre-compiled binaries made available on the Releases Page. However, you must first install the ANTsRCore package, whose pre-compiled binaries are available on its own Releases Page. Download the relevant versions for both pacakges and run this from the command-line:

R CMD INSTALL ANTsRCore_*.tgz R CMD INSTALL ANTsR_*.tgz

From source using devtools

To install ANTsR from source, you can use devtools to install the latest version of the code directly form GitHub. This should also automatically install the main dependencies like the ANTsRCore package.

R devtools::install_github('ANTsX/ANTsR')

From source using R CMD INSTALL

Alternatively, you can clone and install ANTsR and its two main dependencies (ANTsRCore, ITKR) and then install them as you would traditional R source packages.

First, clone the repositories:

sh $ git clone https://github.com/stnava/ITKR.git $ git clone https://github.com/ANTsX/ANTsRCore.git $ git clone https://github.com/ANTsX/ANTsR.git

Install the package as follows:

sh $ R CMD INSTALL ITKR $ R CMD INSTALL ANTsRCore $ R CMD INSTALL ANTsR

Developer notes

Authors

Brian B. Avants (maintainer), Benjamin M. Kandel, Jeff T. Duda, Philip A. Cook, Nicholas J. Tustison

License

Apache License 2.0

Relevant links

ANTsR Instagram

DOI 10.17605/osf.io/bsq5v

Reference manual: ANTsR

Vignettes:

Wiki: Notes and work in progress examples

Package source: from github

Binaries: here

Windows installation option here

Research using ANTsR

Inter-modality inference yet to be added RIPMMARC
Eigenanatomy for multiple modality population studies function sparseDecom
Tumor segmentation function mrvnrfs (not exactly the same but close)
Multiple modality pediatric template and population study employs several aspects of ANTsR
Structural networks from subject-level data function makeGraph plus yet to be added RIPMMARC
SCCAN relating neuroimaging and cognitive batteries function sparseDecom2
Sparse regression with manifold smoothness constraints function sparseRegression
Prior-based eigenanatomy function sparseDecom
Corrective learning for segmentation functions segmentationRefinement.train and segmentationRefinement.predict.
LINDA: automated segmentation of stroke lesions function mrvnrfs.
LESYMAP: lesion to symptom mapping function sparseDecom2.
ANTsRNet A growing collection of well-known deep learning architectures ported to the R language. _ Image segmentation _ U-Net (2-D) _ V-Net (3-D) _ Image classification _ AlexNet (2-D, 3-D) _ Vgg16/Vgg19 (2-D, 3-D) _ ResNet/ResNeXt (2-D, 3-D) _ GoogLeNet (2-D) _ DenseNet (2-D, 3-D) _ Object detection * Single Shot MultiBox Detector (2-D, 3-D)

Contributing

If you have a question or need help solving a problem, please create an issue on GitHub. If you want to contribute code or have a feature request, creating an issue on GitHub is also the best place to start.

Owner

Name: Advanced Normalization Tools Ecosystem
Login: ANTsX
Kind: organization
Location: Cambridge, MA; Philadelphia, PA; Southern California

Website: https://www.ants.dev
Repositories: 8
Profile: https://github.com/ANTsX

Ecosystem supporting multi-modality biomedical image analysis across programming languages.

GitHub Events

Total

Issues event: 18
Watch event: 7
Delete event: 20
Issue comment event: 54
Push event: 105
Pull request event: 40
Create event: 19

Last Year

Issues event: 18
Watch event: 7
Delete event: 20
Issue comment event: 54
Push event: 105
Pull request event: 40
Create event: 19

Committers

Last synced: 9 months ago

All Time

Total Commits: 4,529
Total Committers: 25
Avg Commits per committer: 181.16
Development Distribution Score (DDS): 0.287

Past Year

Commits: 185
Committers: 4
Avg Commits per committer: 46.25
Development Distribution Score (DDS): 0.227

Top Committers

Name	Email	Commits
stnava	s**a@g**m	3,228
muschellij2	m**2@g**m	316
Jeffrey Duda	j**a@g**m	267
Nick Tustison	n**n@g**m	242
Ben Kandel	b**l@s**u	199
Shrinidhi KL	n**i@g**m	87
ncullen93	n**n@m**e	48
armaneshaghi	a**i@g**m	45
dorianps	d****s	38
Philip Cook	c**a@p**u	21
Stefan Schlager	z**2@g**m	7
Tokazama	z**7@g**m	6
dorianps	d**a@c**u	5
stnava	s**a@s**)	4
Zachary Christensen	Z**h@Z**l	3
Chris Hammill	c**l@g**m	2
Nick Cullen	n**1@y**m	2
shrinidhi	s**k@s**)	2
umeshiso	j**s@g**m	1
ArmanEshaghi	m**c@M**l	1
Michael Stauffer	m**f@v**t	1
Nick Tustison	n**n@f**e	1
dorianps	d**a@u**u	1
dorianps	d**a@c**l	1
James Manton	a**n@g**m	1

Committer Domains (Top 20 + Academic)

uphs.upenn.edu: 1 figuring.home: 1 verizon.net: 1 shrik-latitude-e6400.(none): 1 stnava-virtualbox.(none): 1 chead.uphs.upenn.edu: 1 pennmedicine.upenn.edu: 1 med.lu.se: 1 seas.upenn.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 57
Total pull requests: 59
Average time to close issues: 10 months
Average time to close pull requests: 20 days
Total issue authors: 30
Total pull request authors: 4
Average comments per issue: 8.42
Average comments per pull request: 0.58
Merged pull requests: 55
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 11
Pull requests: 36
Average time to close issues: 7 days
Average time to close pull requests: 5 days
Issue authors: 7
Pull request authors: 3
Average comments per issue: 4.64
Average comments per pull request: 0.58
Merged pull requests: 33
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

muratmaga (12)
ptsii (10)
cookpa (4)
JPolzehl (2)
hegde00 (2)
SlicerMorph (2)
baboonsevolve (2)
stnava (1)
ramBrain (1)
adigherman (1)
JinDJsuper (1)
Ali-Mahzarnia (1)
DavidBarriere (1)
qipianmgh (1)
GayanSamuditha (1)

Pull Request Authors

ntustison (46)
cookpa (13)
ncullen93 (10)
muschellij2 (3)

Top Labels

Issue Labels

bug (4) notes about usage (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads: unknown

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 34

proxy.golang.org: github.com/antsx/antsr

Documentation: https://pkg.go.dev/github.com/antsx/antsr#section-documentation
License: apache-2.0
Latest release: v0.6.0
published almost 2 years ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 6 months ago

proxy.golang.org: github.com/ANTsX/ANTsR

Documentation: https://pkg.go.dev/github.com/ANTsX/ANTsR#section-documentation
License: apache-2.0
Latest release: v0.6.0
published almost 2 years ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 5 months ago

Dependencies

DESCRIPTION cran

ANTsRCore >= 0.7.4 depends
R >= 3.0 depends
methods * depends
grDevices * imports
graphics * imports
magrittr * imports
stats * imports
utils * imports
BGLR * suggests
DMwR * suggests
FNN * suggests
MASS * suggests
Matrix * suggests
R.matlab * suggests
Rcpp * suggests
RcppEigen * suggests
RcppHNSW * suggests
abind * suggests
caret * suggests
cluster * suggests
corpcor * suggests
dplyr * suggests
e1071 * suggests
extremevalues * suggests
fastICA * suggests
fpc * suggests
ggplot2 * suggests
glasso * suggests
glmnet * suggests
grid * suggests
hdf5r * suggests
ifultools * suggests
igraph * suggests
irlba * suggests
knitr * suggests
mFilter * suggests
magic * suggests
misc3d * suggests
moments * suggests
networkD3 * suggests
pixmap * suggests
png * suggests
pracma * suggests
psych * suggests
randomForest * suggests
rgl * suggests
rmarkdown * suggests
robust * suggests
robustbase * suggests
rsvd * suggests
signal * suggests
sna * suggests
testthat * suggests
tools * suggests
viridis * suggests
visreg * suggests
wmtsa * suggests
xgboost * suggests

Dockerfile docker

rocker/tidyverse 4.2.3 build

https://github.com/antsx/antsr

Science Score: 59.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Advanced Normalization Tools in R

Installation

Pre-compiled binaries

From source using devtools

From source using R CMD INSTALL

Developer notes

Authors

License

Relevant links

Research using ANTsR

Contributing

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/antsx/antsr

Rankings

proxy.golang.org: github.com/ANTsX/ANTsR

Rankings

Dependencies