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# Release notes


## 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.



# Tagging a beta release

```
git tag -d beta
git push origin :refs/tags/beta
git tag beta
git push --tags origin
```

252 changes: 52 additions & 200 deletions README.md
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[ANTsR Instagram](https://www.instagram.com/antsrx/)


<!--
![ants brain](http://i.imgur.com/I2VNWpA.png)
![ants edie](http://i.imgur.com/DcV1NVT.png)
![ants babe](http://i.imgur.com/gwoxI5M.png)
-->
# ANTsR

[DOI 10.17605/osf.io/bsq5v](https://osf.io/bsq5v/)
# Advanced Normalization Tools in R

![Downloads](https://img.shields.io/github/downloads/antsx/antsr/total)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/stnava/ANTsRDocker/master)
[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](code_of_conduct.md)

<br />

ANTsR is an R package which wraps the well-established C++ biomedical image processing library <i>[ANTs](https://github.com/ANTsX/ANTs)</i>. 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](https://github.com/ANTsX/ANTsPy) which provides pre-trained models and utilities for training deep learning models on medical images.

<br />

## Installation

Currently, the only way to install ANTsR is from the pre-compiled binaries or from source. We are actively working on getting ANTsR onto CRAN / Bioconductor / etc.

### Binaries

The fastest way to install ANTsR is from pre-compile binaries. Download the relevant version and run this from the command-line:

```
R CMD INSTALL ANTsR_*.tgz
```

### From source using devtools

<!-- commenting out because we moved to antsx
[![Coverage Status](https://coveralls.io/repos/stnava/ANTsR/badge.svg)](https://coveralls.io/r/stnava/ANTsR)
[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/stnava/ANTsR?branch=master&svg=true)](https://ci.appveyor.com/project/stnava/ANTsR) -->
To install ANTsR from source, you can use devtools to install the latest version of the code directly form GitHub:

A package providing [ANTs](https://github.com/ANTsX/ANTs) features in R as well as imaging-specific data representations, spatially regularized dimensionality reduction and segmentation tools. See also the **Neuroconductor** [site](https://www.neuroconductor.org/package/details/ANTsR).
```R
devtools::install_github('ANTsX/ANTsR')
```

### From source using R CMD INSTALL

## Description
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.

License: Apache License 2.0
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
```

Maintainer: [Brian B. Avants](http://stnava.github.io/)
Install the package as follows:

URL: [homepage](https://antsx.github.io/ANTsR/)
```sh
$ R CMD INSTALL ITKR
$ R CMD INSTALL ANTsRCore
$ R CMD INSTALL ANTsR
```

BugReports: [github issues](http://github.com/ANTsX/ANTsR/issues)
## Developer notes

NeedsCompilation: yes
### Maintainer

Travis checks: [ANTsR results](https://travis-ci.org/ANTsX/ANTsR)
[Brian B. Avants](http://stnava.github.io/)

Documentation: [https://antsx.github.io/ANTsR/](https://antsx.github.io/ANTsR/).
### License

## Preview ANTsR on the cloud
Apache License 2.0

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.
## Relevant links

## Downloads
[ANTsR Instagram](https://www.instagram.com/antsrx/)

[DOI 10.17605/osf.io/bsq5v](https://osf.io/bsq5v/)

Reference manual: [ANTsR](https://antsx.github.io/ANTsR/reference/index.html)

Expand All @@ -58,11 +90,6 @@ Binaries: [here](http://github.com/ANTsX/ANTsR/releases/)

**Suggested packages** [https://github.com/stnava/ANTsRDocker/blob/master/install.R](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

Expand Down Expand Up @@ -101,178 +128,3 @@ architectures ported to the R language.
* DenseNet (2-D, 3-D)
* Object detection
* Single Shot MultiBox Detector (2-D, 3-D)

## Installation from source

Please read this entire section before choosing which method you prefer.

In general, these **assume** you have [git](http://git-scm.com/) installed / accessible in your environment, as well as a compiler, preferably `clang`. you may also need [cmake](http://www.cmake.org) if you do/can not install `cmaker`.

Windows users should see [Rtools](http://cran.r-project.org/bin/windows/Rtools/) and maybe, also, [installr](https://github.com/talgalili/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](https://github.com/stnava/ITKR/releases) and [here](https://github.com/ANTsX/ANTsRCore/releases) 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](https://github.com/ANTsX/ANTsR/blob/master/DESCRIPTION) under `Suggests`.
A complete list of recommended ancillary packages [here](https://github.com/ANTsX/ANTsR/wiki/ANTsR-Dependencies-for-(close-to)-full-functionality).

**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:
```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
```

The [`travis.yml` file](https://github.com/ANTsX/ANTsR/blob/master/.travis.yml) 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](https://github.com/rocker-org/rocker/wiki/Using-the-RStudio-image)

* 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 of `antsr`

* 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](http://yihui.name/en/2013/06/r-package-versioning/). 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.

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