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============================
Advanced Normalization Tools
============================
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)
Email: [antsr.me at gmail dot com](mailto:antsr.me@gmail.com)
Install ANTs via pre-built:
[Packages](http://sourceforge.net/projects/advants/files/ANTS/)
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](http://testing.psychiatry.uiowa.edu/CDash/index.php?project=ANTS) maintained by 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.
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), Jeffrey T. Duda (DTI), Ben M. Kandel (Perfusion, multivariate analysis), Kent Williams (software engineer, UIowa)
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
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
----------------------------------------------------------
- New *antsRegistration* [bash
example](https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh)
- New *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 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)
- Nick led us to a win at the [BRATS 2013 challenge](http://martinos.org/qtim/miccai2013/) with [ANTsR](http://stnava.github.io/ANTsR/)
Learning about ANTs
----------------------------------------------------------
**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/)
**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)
**MALF labeling example** [example](https://github.com/ntustison/MalfLabelingExample)
**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)
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)
ANTs was supported by: R01-EB006266-01
[](http://githalytics.com/stnava/ANTs)
|
