# ANTs-github **Repository Path**: dengjiayang/ants-github ## Basic Information - **Project Name**: ANTs-github - **Description**: No description available - **Primary Language**: Unknown - **License**: BSD-3-Clause - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2021-10-27 - **Last Updated**: 2024-04-26 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README [Advanced Normalization Tools](https://imgur.com/a/kySGi) ========================================================= [![Build Status](https://travis-ci.org/ANTsX/ANTs.svg?branch=master)](https://travis-ci.org/ANTsX/ANTs) [![ANTsX](https://circleci.com/gh/ANTsX/ANTs.svg?style=shield)](https://app.circleci.com/pipelines/github/ANTsX/ANTs) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](code_of_conduct.md) ANTs computes high-dimensional mappings to capture the statistics of brain structure and function. See the [collection of examples at this 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](https://github.com/ANTsX/ANTsR) is the underlying statistical workhorse. ANTsR examples [here](https://rpubs.com/antsr). [ANTsPy](https://github.com/ANTsX/ANTsPy) is pythonic ANTs/ANTsR. See [this content too](https://github.com/stnava/ANTsRPy). 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/). The [ANTs handout](https://github.com/stnava/ANTsTutorial/raw/master/handout/antsHandout.pdf), part of forthcoming [ANTs tutorial](https://github.com/stnava/ANTsTutorial) material [here](https://github.com/stnava/ANTsTutorial) and [here](https://rpubs.com/antsr/). [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. You can also run ANTs Cortical Thickness pipeline in the cloud using the free [http://OpenNeuro.org](OpenNeuro.org) platform (no installation required). Build [ANTs](https://github.com/stnava/ANTs) from: Source-Code (recommended) on [Linux / Mac OS](https://github.com/stnava/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS) or [Windows](https://github.com/stnava/ANTs/wiki/Compiling-ANTs-on-Windows-10). 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)](https://scholar.google.com/scholar?q=joint+label+fusion+yushkevich&btnG=&hl=en&as_sdt=0%2C31) and [JLF](http://journal.frontiersin.org/article/10.3389/fninf.2013.00027/full), 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 (examples, etc.) ---------------------------------------------------------- ### General * **antsRegistration** [bash example](https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh) * **antsRegistration with mask** [(bash, ANTsR and ANTsPy examples)](https://github.com/ntustison/antsRegistrationWithMaskExample) * **ANTs and ITK** [paper](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009425/) * **Large deformation** [(bash, ANTsR and ANTsPy examples)](http://stnava.github.io/C/) * **Automobile** [(bash and ANTsR examples)](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 ... * **Global optimization** [example](http://stnava.github.io/butterfly/) * **Patch-based super resolution** [example](https://github.com/ntustison/NonLocalSuperResolutionExample) * **Image denoising** [(bash, ANTsR and ANTsPy examples)](https://github.com/ntustison/DenoiseImageExample) * **Visualization** [example](https://github.com/ntustison/antsVisualizationExamples) * **Morphing** [example](http://stnava.github.io/Morpheus/) * **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) ### Neuro * **Basic Brain Mapping** [(bash and ANTsR examples)](http://stnava.github.io/BasicBrainMapping/) * **Template construction** [(bash, ANTsR and ANTsPy examples)](http://ntustison.github.io/TemplateBuildingExample/) * **Single subject template construction** [example](https://github.com/ntustison/SingleSubjectTemplateExample) * **Pre-built ANTs templates with spatial priors** [download](http://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436) including an [MNI version](https://figshare.com/articles/ANTs_files_for_mni_icbm152_nlin_sym_09a/8061914). * **Brain extraction** [(bash and ANTsR examples)](https://github.com/ntustison/antsBrainExtractionExample) * **N4 bias correction <-> segmentation** [(bash, ANTsR and ANTsPy examples)](https://github.com/ntustison/antsAtroposN4Example) * **Cortical thickness** [example](https://github.com/ntustison/antsCorticalThicknessExample) * **"Cooking" tissue priors for templates** [example](https://github.com/ntustison/antsCookTemplatePriorsExample) (after you build your template) * **Multi-atlas joint label/intensity fusion examples** [(bash and ANTsR examples 1)](https://github.com/ntustison/MalfLabelingExample) [example 2](https://github.com/qureai/Multi-Atlas-Segmentation) (thanks to @chsasank) * **The ANTs Cortical Thickness Pipeline** [example](https://github.com/ntustison/KapowskiChronicles/blob/master/paper2.pdf?raw=true) * **Chimpanzee cortical thickness** [example](https://github.com/stnava/WHopkinsNHP/) * **Brain tumor segmentation** [example](https://github.com/ntustison/BRATS2013/SimpleExample/) * **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) * **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 ... * **Partial EPI slab to T1 image registration** [example](https://github.com/ntustison/PartialSlabEpiT1ImageRegistration) ### Lung * **CT lung registration** [(bash and ANTsR examples)](https://github.com/ntustison/antsCtLungRegistrationExample) * **Lung mask registration** [example](https://github.com/ntustison/ProtonCtLungMaskRegistration) * **Lung and lobe estimation** [example](https://github.com/ntustison/LungAndLobeEstimationExample) * **Lung ventilation-based segmentation** [example](https://github.com/ntustison/LungVentilationSegmentationExample) ### Cardiac * **Cardiac** [example](http://stnava.github.io/LabelMyHeart) ### Misc. 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** for expected memory and computation time: [results](https://github.com/gdevenyi/antsRegistration-benchmarking). These results are, of course, system and data dependent. 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)