From de56d803580ea1e05ccf79638046f0405c7421fd Mon Sep 17 00:00:00 2001 From: stnava Date: Thu, 31 Aug 2017 07:33:27 -0400 Subject: [PATCH] Set theme jekyll-theme-midnight and migrate Page Generator content --- _config.yml | 8 ++ index.md | 342 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 350 insertions(+) create mode 100644 _config.yml create mode 100644 index.md diff --git a/_config.yml b/_config.yml new file mode 100644 index 000000000..608290680 --- /dev/null +++ b/_config.yml @@ -0,0 +1,8 @@ +title: ANTs +description: Advanced Normalization Tools +google_analytics: "47460530" +show_downloads: true +theme: jekyll-theme-midnight + +gems: + - jekyll-mentions diff --git a/index.md b/index.md new file mode 100644 index 000000000..e504157c3 --- /dev/null +++ b/index.md @@ -0,0 +1,342 @@ + +============================ +[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.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)