ANTsR
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R interface to the ANTs biomedical image processing library
ANTsR
A package providing ANTs features in R as well as imaging-specific data representations, spatially regularized dimensionality reduction and segmentation tools. See also the Neuroconductor site.
Description
License: Apache License 2.0
Maintainer: Brian B. Avants
URL: homepage
BugReports: github issues
NeedsCompilation: yes
Travis checks: ANTsR results
Documentation: https://antsx.github.io/ANTsR/.
Preview ANTsR on the cloud
Try the binder link above.
Note: as of this writing, memory is very limited on this cloud preview so some examples may not run successfully.
Downloads
Reference manual: ANTsR
Wiki: Notes and work in progress examples
Package source: from github
Binaries: here
Windows installation option here
Suggested packages https://github.com/stnava/ANTsRDocker/blob/master/install.R
Install the binary, after downloading, via command line:
R CMD INSTALL ANTsR_*.tgz
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
andsegmentationRefinement.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)
- Image segmentation
Installation from source
Please read this entire section before choosing which method you prefer.
In general, these assume you have git installed / accessible in your environment, as well as a compiler, preferably clang
. you may also need cmake if you do/can not install cmaker
.
Windows users should see Rtools and maybe, also, installr for assistance in setting up their environment for building (must have a compiler too). To my knowledge, there are no recorded instances of ANTsR being installed on Windows. If someone does so, we would like to know.
You will need to install R packages that ANTsR requires. Minimally: Install ITKR and ANTsRCore here and here then do:
mydeps <- c( "Rcpp", "RcppEigen", "magrittr", "rsvd", "magic", "psych" )
install.packages( pkgs = mydeps, dependencies = TRUE )
You can gain additional functionality by installing packages that
are listed in the DESCRIPTION
file under Suggests
.
A complete list of recommended ancillary packages here.
Method 1: with devtools in R
library( devtools )
# install_github("stnava/cmaker") # if you do not have cmake
install_github("stnava/ANTsR")
Method 2: from command line (most traditional method)
Assumes git, cmake and compilers are available in your environment (as above).
First, clone the repository:
$ 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:
$ R CMD INSTALL ITKR
$ R CMD INSTALL ANTsRCore
$ R CMD INSTALL ANTsR
The travis.yml
file also shows a way to install from Linux command line.
Method 3: from binaries
Note that version numbers will change over time.
wget https://github.com/stnava/ITKR/releases/download/latest/ITKR_0.4.12_R_x86_64-pc-linux-gnu.tar.gz
R CMD INSTALL ITKR_0.4.12_R_x86_64-pc-linux-gnu.tar.gz
wget https://github.com/ANTsX/ANTsRCore/releases/download/v0.4.2.1/ANTsRCore_0.4.2.1_R_x86_64-pc-linux-gnu.tar.gz
R CMD INSTALL ANTsRCore_0.4.2.1_R_x86_64-pc-linux-gnu.tar.gz
wget https://github.com/ANTsX/ANTsR/releases/download/latest/ANTsR_0.6_R_x86_64-pc-linux-gnu.tar.gz
R CMD INSTALL ANTsR_0.6_R_x86_64-pc-linux-gnu.tar.gz
Method 4: platform independent via docker and kitematic
This is a beta operation that is in flux but may be convenient for some users.
-
based on this approach
-
create a docker username
-
download and install kitematic
-
login to kitematic with your docker username
-
search for
antsr
in the kitematic repository search bar -
create a new container from the
stnava
version ofantsr
-
start the container
-
type the "access url" address into a browser to run rstudio with antsr. it should be something like
http://192.168.99.100:32989/
-
you can also add your home folders to the container instance by adjusting the "volumes" option under the settings tab. then you can access local data.
Usage
Load the package:
library(ANTsR)
List the available functions in the namespace ANTsR:
ANTsR::<double-tab>
Call help on a function via ?functionName or see function arguments
via args(functionName)
Tagging a beta release
git tag -d beta
git push origin :refs/tags/beta
git tag beta
git push --tags origin
Release notes
More like development highlights, as opposed to release notes. See git log
for the complete history. We try to follow these versioning recommendations for R packages. Under these guidelines, only major.minor
is an official release.
0.4.0
- ENH: better compilation and release style.
- ENH: return boolean same size as image
- ENH: improved decomposition methods
- ENH: easier to use antsrSurf and antsrVol
0.3.3
- ENH: spare distance matrix, multi scale svd
0.3.2
-
ENH: added domainImg option to plot.antsImage which can standardize plot.
-
COMP: test for DVCL define requirement to improve clang and gcc compilations
-
WIP: transform objects can be created on the fly and manipulated thanks to jeff duda
-
ENH: automation for eigenanatomy
-
ENH: reworked SCCAN and eanat
-
ENH: mrvnrfs
-
ENH: resting state Vignette
-
DOC: clarify/extend antsApplyTransforms
-
ENH: multidimensional images
-
STYLE: iMath not ImageMath in ANTsR
0.3.1
-
WIP: iMath improvements
-
WIP: ASL pipeline fuctionality
-
BUG: Fixed image indexing bug
-
BUG: plot.antsImage improvements
-
ENH: more antsRegistration options
-
ENH: geoSeg
-
ENH: JointLabelFusion and JointIntensityFusion
-
ENH: Enable negating images
-
ENH: weingarten curvature
-
ENH: antsApplyTransformsToPoints with example
-
ENH: renormalizeProbabilityImages
-
ENH: Suppress output from imageWrite.
0.3.0
First official release.