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+title: ANTs
+description: Advanced Normalization Tools
+google_analytics: "47460530"
+show_downloads: true
+theme: jekyll-theme-midnight
+
+gems:
+  - jekyll-mentions

index.md

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+<!--
+![ants registration artillery](http://i.imgur.com/FCLrXV1.jpg)
+![ants multivar](http://i.imgur.com/YqWtunL.png)
+![ants faces](http://i.imgur.com/wBOFGwg.png)
+![ants goat](http://i.imgur.com/SEKf1mo.jpg) -->
+============================
+[Advanced Normalization Tools](https://imgur.com/a/kySGi)
+============================
+
+[![Build Status](https://travis-ci.org/stnava/ANTs.svg?branch=master)](https://travis-ci.org/stnava/ANTs)
+
+ANTs computes high-dimensional mappings to capture the statistics of brain
+structure and function.  See the [FAQ page](https://github.com/stnava/ANTsTutorial/blob/master/handout/antsGithubExamples.Rmd).
+
+![ants template](http://i.imgur.com/mLZ71Ai.png)
+
+ANTs allows one to organize, visualize and statistically explore large biomedical
+image sets.
+
+![ants render](http://i.imgur.com/hMW6fjB.png)
+
+ANTs integrates imaging modalities and related information in space and time.
+
+![ants render](http://i.imgur.com/oIMrnpY.png)
+
+ANTs works across species or organ systems with minimal customization.
+
+![ants primate](http://i.imgur.com/Dfrifgg.png)
+
+ANTs and related tools have won several international and unbiased competitions.
+
+![ants competes](http://i.imgur.com/HE0j7IC.png)
+
+[ANTsR](http://stnava.github.io/ANTsR/) is the underlying statistical workhorse.
+
+Questions: [Discussion Site](http://sourceforge.net/p/advants/discussion/) or *new* [ANTsDoc](http://stnava.github.io/ANTsDoc/) or try [this version](http://issuu.com/brianavants/docs/ants2) ... also read our [guide to evaluation strategies and addressing new problems with ANTs or other software](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766821/).  *New* [ANTs handout](https://github.com/stnava/ANTsTutorial/raw/master/handout/antsHandout.pdf), part of forthcoming [ANTs tutorial]() material.
+
+[ANTsTalk - subject to change at any moment](http://stnava.github.io/ANTsTalk/)
+
+[ANTsRegistrationTalk - subject to change at any moment](http://stnava.github.io/ANTsRegistrationTalk/)
+
+ Install ANTs via pre-built:
+[Packages @ github](https://github.com/stnava/ANTs/releases) older
+versions [@ sourceforge](http://sourceforge.net/projects/advants/files/ANTS/) ... also,
+[Github Releases are here](https://github.com/stnava/ANTs/releases) thanks to Arman Eshaghi.
+
+ Build [ANTs](https://github.com/stnava/ANTs) from:
+[Source-Code](http://brianavants.wordpress.com/2012/04/13/updated-ants-compile-instructions-april-12-2012/)
+(recommended)
+
+[ANTs Dashboard](https://travis-ci.org/stnava/ANTs/) thanks to Arman Eshaghi and  Hans J. Johnson
+
+ANTs extracts information from complex datasets that include imaging
+([Word Cloud](http://brianavants.files.wordpress.com/2013/05/avants_wordcloud.jpg)).
+Paired with [ANTsR](http://stnava.github.io/software/2014/01/08/antsr/) (answer), ANTs is
+useful for managing, interpreting and visualizing multidimensional data.
+ANTs is
+[popularly](https://sourceforge.net/projects/advants/files/ANTS/stats/timeline?dates=2010-07-19+to+2099-05-25)
+considered a state-of-the-art medical image registration and
+segmentation toolkit. ANTsR is an emerging tool supporting standardized
+multimodality image analysis. ANTs depends on the Insight ToolKit
+[(ITK)](http://www.itk.org), a widely used medical image processing
+library to which ANTs developers contribute.  A summary of some ANTs findings and tutorial material (most of which is on this page) is [here](http://rpubs.com/stnava/ANTsTut).
+
+Authors
+-------
+
+### Brian B. Avants - UPENN
+
+**Role:** Creator, Algorithm Design, Implementation,
+[more](http://stnava.github.io/Resume/)
+
+### Nicholas J. Tustison - UVA
+
+**Role:** Compeller, Algorithm Design, Implementation Guru,
+[more](http://ntustison.github.io/CV/)
+
+### Hans J. Johnson - UIowa
+
+**Role:** Large-Scale Application, Testing, Software design
+
+### Team Members
+
+**Core:** Gang Song (Originator), Philip A. Cook, Jeffrey T. Duda (DTI), Ben M. Kandel (Perfusion, multivariate analysis)
+
+Image Registration
+------------------
+
+Diffeomorphisms: [SyN](http://www.ncbi.nlm.nih.gov/pubmed/17659998),
+Independent Evaluation:
+[Klein](http://www.ncbi.nlm.nih.gov/pubmed/19195496),
+[Murphy](http://www.ncbi.nlm.nih.gov/pubmed/21632295), Template
+Construction
+[(2004)](http://www.ncbi.nlm.nih.gov/pubmed/15501083)[(2010)](http://www.ncbi.nlm.nih.gov/pubmed/19818860),
+[Similarity Metrics](http://www.ncbi.nlm.nih.gov/pubmed/20851191),
+[Multivariate
+registration](http://www.ncbi.nlm.nih.gov/pubmed/18995188), [Multiple
+modality analysis and statistical
+bias](http://www.ncbi.nlm.nih.gov/pubmed/23151955)
+
+Image Segmentation
+------------------
+
+Atropos Multivar-EM Segmentation
+[(link)](http://www.ncbi.nlm.nih.gov/pubmed/21373993), Multi-atlas
+methods [(link)](http://www.ncbi.nlm.nih.gov/pubmed/21237273N4), Bias
+Correction [(link)](http://www.ncbi.nlm.nih.gov/pubmed/20378467), DiReCT
+cortical thickness
+[(link)](http://www.ncbi.nlm.nih.gov/pubmed/19150502), DiReCT in
+[chimpanzees](http://www.ncbi.nlm.nih.gov/pubmed/23516289)
+
+Multivariate Analysis Eigenanatomy [(1)](http://www.ncbi.nlm.nih.gov/pubmed/23286132) [(2)](http://www.ncbi.nlm.nih.gov/pubmed/23475817)
+----------------------------------------------------------------------------------------------------------------------------------------
+
+Prior-Based Eigenanatomy [(in
+prep)](http://www.ncbi.nlm.nih.gov/pubmed/?), Sparse CCA
+[(1)](http://www.ncbi.nlm.nih.gov/pubmed/20083207),
+[(2)](http://www.ncbi.nlm.nih.gov/pubmed/20879247), Sparse Regression
+[(link)](http://link.springer.com/chapter/10.1007%2F978-3-642-38868-2_8)
+
+ImageMath Useful!
+-----------------
+
+morphology, GetLargestComponent, CCA, FillHoles ... much more!
+
+Application Domains
+-------------------
+
+### Frontotemporal degeneration [PENN FTD center](http://ftd.med.upenn.edu)
+
+### Multimodality Neuroimaging
+
+-   [Structural MRI](http://jeffduda.github.io/NeuroBattery/)
+-   Functional MRI
+-   Network Analysis
+
+### Lung Imaging
+
+-   Structure
+-   Perfusion MRI
+-   Branching
+
+### Multiple sclerosis (lesion filling) [example](https://github.com/armaneshaghi/LesionFilling_example)
+
+Background & Theory
+----------------------------------------------------------
+
+-   The
+    [SyN](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22SyN%22+AND+%22Avants+B%22)
+    and [N4 bias
+    correction](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22N4%22+AND+%22Tustison+N4ITK%22)
+    papers and other relevant references in
+    [Pubmed](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Tustison+N%22+AND+%22Avants+B%22)
+
+-   Visualization: e.g. [a gource of ANTs
+    development](http://vimeo.com/66781467)
+
+-   [DiReCT](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22DIRECT%22+AND+%22Avants%22+AND+DAS)
+    cortical thickness
+    [papers](http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Cortical+Thickness%22+AND+%22Avants%22)
+
+-   A
+    [folder](https://sourceforge.net/projects/advants/files/Documentation/)
+    of relevant docs:
+    [segmentation](http://sourceforge.net/projects/advants/files/Documentation/atropos.pdf/download),
+    [registration](http://sourceforge.net/projects/advants/files/Documentation/antstheory.pdf/download),
+    [usage(old)](http://sourceforge.net/projects/advants/files/Documentation/ants.pdf/download),
+    [for clinical
+    apps](http://sourceforge.net/projects/advants/files/Documentation/ANTSMethodologySummary.docx/download)
+
+-   ANTs redesigned for generality, automation, multi-core computation
+    with ITKv4
+
+-   Dev'd ITKv4 with Kitware, GE, Natl. Lib of Medicine & Academia
+
+
+ANTs has won several unbiased & international competitions
+----------------------------------------------------------
+
+-   ANTs finished in 1st rank in [Klein 2009 intl. brain mapping
+    competition](http://www.ncbi.nlm.nih.gov/pubmed/19195496)
+
+-   ANTs finished 1st overall in [EMPIRE10 intl. lung mapping
+    competition](http://www.ncbi.nlm.nih.gov/pubmed/21632295)
+
+-   ANTs is the standard registration for
+    [MICCAI-2013](http://www.miccai2013.org/) segmentation competitions
+
+-   Conducting ANTs-based R tutorial @ MICCAI-2013
+
+-   ITK-focused Frontiers in Neuroinformatics research topic
+    [here](http://www.frontiersin.org/neuroinformatics/researchtopics/neuroinformatics_with_the_insi/1580)
+
+-   Won the [BRATS 2013 challenge](http://martinos.org/qtim/miccai2013/) with [ANTsR](http://stnava.github.io/ANTsR/)
+
+-   Won the best paper award at the [STACOM 2014 challenge](http://www.cardiacatlas.org/web/stacom2014/home)
+
+Learning about ANTs
+----------------------------------------------------------
+**antsRegistration** [bash example](https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh)
+
+**Eigenanatomy** for [multivariate neuroimage analysis](http://www.ncbi</a>.nlm.nih.gov/pubmed/23269595) via
+    [PCA](http://www.ncbi.nlm.nih.gov/pubmed/23286132) &
+    [CCA](http://www.ncbi.nlm.nih.gov/pubmed/20083207)
+
+**ANTs and ITK** [paper](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009425/)
+
+**Pre-built ANTs templates with spatial priors** [download](http://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436)
+
+**The ANTs Cortical Thickness Pipeline** [example](https://github.com/ntustison/KapowskiChronicles/blob/master/paper2.pdf?raw=true)
+
+**"Cooking" tissue priors for templates**
+  [example](https://github.com/ntustison/antsCookTemplatePriorsExample)
+  (after you build your template)
+
+**Basic Brain Mapping** [example](http://stnava.github.io/BasicBrainMapping/)
+
+**Large deformation** [example](http://stnava.github.io/C/)
+
+**Template construction** [example](http://ntustison.github.io/TemplateBuildingExample/)
+
+**Automobile** [example](http://stnava.github.io/cars/)
+
+**Asymmetry** [example](http://stnava.github.io/asymmetry/)
+
+**Point-set** [mapping](http://stnava.github.io/chicken/) which includes the
+PSE metric and affine and deformable registration with (labeled) pointsets or
+iterative closest point
+
+**Feature matching** [example](http://stnava.github.io/featureMatching/) ... not up to date ...
+
+**Chimpanzee cortical thickness** [example](https://github.com/stnava/WHopkinsNHP/)
+
+**Global optimization** [example](http://stnava.github.io/butterfly/)
+
+**Morphing** [example](http://stnava.github.io/Morpheus/)
+
+**fMRI or Motion Correction** [example](http://stnava.github.io/fMRIANTs/)
+
+**fMRI reproducibility** [example](http://stnava.github.io/RfMRI/)
+
+**fMRI prediction** [example](http://stnava.github.io/Haxby2001/) ... WIP ...
+
+**Cardiac** [example](http://stnava.github.io/LabelMyHeart)
+
+**Brain extraction** [example](https://github.com/ntustison/antsBrainExtractionExample)
+
+**N4 bias correction <-> segmentation** [example](https://github.com/ntustison/antsAtroposN4Example)
+
+**Cortical thickness** [example](https://github.com/ntustison/antsCorticalThicknessExample)
+
+**Multi-atlas joint label/intensity fusion examples** [example 1](https://github.com/ntustison/MalfLabelingExample) [example 2](https://github.com/qureai/Multi-Atlas-Segmentation) (thanks to @chsasank)
+
+**Lung and lobe estimation** [example](https://github.com/ntustison/LungAndLobeEstimationExample)
+
+**Bibliography** [bibtex of ANTs-related papers](https://github.com/stnava/ANTsBibliography)
+
+**ANTs** [google scholar page](http://scholar.google.com/citations?user=ox-mhOkAAAAJ&hl=en)
+
+Presentations: e.g. [a Prezi about
+ANTs](http://prezi.com/mwrmcm-h9-w4/ants/?kw=view-mwrmcm-h9-w4&rc=ref-40024395)
+(WIP)
+
+Reproducible science as a teaching tool: e.g. [compilable ANTs
+tutorial](https://github.com/stnava/ANTS_MultiModality) (WIP)
+
+Other examples [slideshow](http://brianavants.wordpress.com)
+
+Landmark-based mapping for e.g. hippocampus [discussed
+here](https://sourceforge.net/p/advants/discussion/840261/thread/1cb7b165/?limit=50)
+
+Brief ANTs segmentation [video](http://vimeo.com/67814201)
+
+**Benchmarks** [results](https://github.com/gdevenyi/antsRegistration-benchmarking)
+
+References
+----------------------------------------------------------
+
+[Google
+Scholar](http://scholar.google.com/scholar?q=Advanced+Normalization+Tools+%22ANTs%22+-ant&hl=en&as_sdt=1%2C39&as_ylo=2008&as_yhi=)
+
+[Pubmed](http://www.ncbi.nlm.nih.gov/pubmed?term=%22Avants%20B%22%20OR%20%22Tustison%20N%22)
+
+Boilerplate ANTs
+------------------
+
+Here is some boilerplate regarding ants image processing:
+
+We will analyze multiple modality neuroimaging data with Advanced
+Normalization Tools (ANTs) version >= 2.1 [1]
+(http://stnava.github.io/ANTs/).  ANTs has proven performance in
+lifespan analyses of brain morphology [1] and function [2] in both
+adult [1] and pediatric brain data [2,5,6] including infants [7].
+ANTs employs both probabilistic tissue segmentation (via Atropos [3])
+and machine learning methods based on expert labeled data (via joint
+label fusion [4]) in order to maximize reliability and consistency of
+multiple modality image segmentation.  These methods allow detailed
+extraction of critical image-based biomarkers such as volumes
+(e.g. hippocampus and amygdala), cortical thickness and area and
+connectivity metrics derived from structural white matter [13] or
+functional connectivity [12]. Critically, all ANTs components are
+capable of leveraging multivariate image features as well as expert
+knowledge in order to learn the best segmentation strategy available
+for each individual image [3,4].  This flexibility in segmentation and
+the underlying high-performance normalization methods have been
+validated by winning several internationally recognized medical image
+processing challenges conducted within the premier conferences within
+the field and published in several accompanying articles
+[8][9][10][11].
+
+References
+
+[1] http://www.ncbi.nlm.nih.gov/pubmed/24879923
+
+[2] http://www.ncbi.nlm.nih.gov/pubmed/24817849
+
+[3] http://www.ncbi.nlm.nih.gov/pubmed/21373993
+
+[4] http://www.ncbi.nlm.nih.gov/pubmed/21237273
+
+[5] http://www.ncbi.nlm.nih.gov/pubmed/22517961
+
+[6] http://www.ncbi.nlm.nih.gov/pubmed/24033570
+
+[7] http://www.ncbi.nlm.nih.gov/pubmed/24139564
+
+[8]  http://www.ncbi.nlm.nih.gov/pubmed/21632295
+
+[9] http://www.ncbi.nlm.nih.gov/pubmed/19195496
+
+[10] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837555/
+
+[11] http://nmr.mgh.harvard.edu/~koen/MenzeTMI2014.pdf
+
+[12] http://www.ncbi.nlm.nih.gov/pubmed/23813017
+
+[13] http://www.ncbi.nlm.nih.gov/pubmed/24830834
+
+
+ANTs was supported by: R01-EB006266-01 and by K01-ES025432-01
+
+![ants chimp](http://i.imgur.com/4tPvy05.png)