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antsGithubExamples.Rmd
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antsGithubExamples.Rmd
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---
title: "Advanced Normalization Tools: <br> Examples that answer FAQs"
author: "Brian B. Avants"
date: "`r Sys.Date()`"
output: html_document
---
# Introduction
[Advanced Normalization Tools](https://github.com/stnava/ANTs) uses [github](www.github.com) to organize and
distribute simple, reproducible examples. We also provide a [wiki](https://github.com/stnava/ANTs/wiki) and the indispensable [antsHandout](https://github.com/stnava/ANTsTutorial/raw/master/handout/antsHandout.pdf). We also perform [tutorials](https://github.com/stnava/ANTsTutorial) when invited to do so.
# Wiki examples
| Short name | link | Comments |
|---|---|---|
| antscall| http://bit.ly/2hzISPF | details what the ants command line means |
| antsvers | http://bit.ly/2h3FN9M | identify your ants version |
| act | http://bit.ly/2hR4giy | what do these programs ants\*CorticalThickness.sh produce? |
| build | http://bit.ly/2gEkDOo | how do i build ants? |
| win-build | http://bit.ly/2holAP2 | how do i build ants on windows? |
| nifti | http://bit.ly/2hongIt | How does ANTs handle qform and sform in NIFTI 1 images? |
| amzn | http://bit.ly/2gOmHqt | Can I install ANTs on Amazon? |
| regerr | http://bit.ly/2hRcOGm | How do I interpret a registration error? |
| orient | http://bit.ly/2hR4oP4 | Why is my image orientation incorrect? |
| mmm | http://bit.ly/2h3DsMa | Brief multiple modality mapping of fMRI to a template space via transform concatenation |
| regFAQ | http://bit.ly/2hojxe1 | Registration FAQ |
| snap | http://bit.ly/2hJcTzK | ITK-snap suggestions |
| DTI | http://bit.ly/2h3KS1P | transform DTI |
| RegMask | http://bit.ly/2hRcNlD | ``antsRegistration`` with mask |
| | | |
# ANTsR: reproducible science with bioimaging data
[ANTsR](https://github.com/stnava/ANTsR) illustrates several use cases throughout its [vignettes and documentation](https://github.com/stnava/ANTsR/releases/tag/latest). Built in the style of *R*, most if not all ANTsR functions are accompanied by reproducible examples. See, for instance, `?antsRegistration` in ANTsR. Soon, [*Neuroconductor*](https://neuroconductor.org/) will also be a source of help.
# Links to github examples with brief comments
These are different than wiki examples in that they come with data.
A user interested in these examples should *clone* the repository via *git*.
```{bash,eval=FALSE}
git clone reponame.git
```
The repository will show you how to do this, otherwise search for the answer from the cloud.
| Short name | link | Comments |
|---|---|---|
| begin | https://github.com/stnava/alphANTs | very basic registration and core tool examples |
| chicken | https://github.com/stnava/chicken | mapping points and global optimization |
| template | https://github.com/ntustison/TemplateBuildingExample | build an optimal template as in many different <br> ants papers that allow large-scale brain mapping |
| visualization | https://github.com/ntustison/antsVisualizationExamples | volumetric and surface-based rendering for images and overlays |
| ICA-eigenanatomy | https://github.com/stnava/blindSourceSeparationInANTsR | Reproduces a classic example in blind source separation and shows how to link with eigenanatomy |
| BBM | https://github.com/stnava/BasicBrainMapping | A simple and "fast" brain registration example |
| jacobian | https://github.com/stnava/jacobianTests | very basic test of jacobian |
| sccan | https://github.com/stnava/sccanTutorial | introduction to sparse canonical correlation analysis statistical studies - may be slightly out of date |
| RMI | https://github.com/stnava/RMI | R in medical imaging tutorial material |
| RMID | https://github.com/stnava/RMI_Data | data for RMI |
| morphing | https://github.com/stnava/Morpheus | morphing example with antsRegistration |
| ASL | https://github.com/stnava/antsASLProcessing | arterial spin labeling (ASL) processing pipeline using ANTs. |
| ANTsDoc | https://github.com/stnava/ANTsDoc | Documentation for ANTs |
| ANTsMM | https://github.com/stnava/ANTS_MultiModality | older talk on multiple modality ANTs processing |
| fMRIANTs | https://github.com/stnava/fMRIANTs | Minimal fMRI pre-processing with ANTS, may be slightly out of date |
| featureMatching | https://github.com/stnava/featureMatching | old example of SIFT-like feature matching, subsumed by antsAI |
| NB | https://github.com/stnava/NeuroBattery | Using ANTs to process multiple MR image types for a single subject |
| Eanat1 | https://github.com/stnava/eigenanatomy1 | basic eigenanatomy example in aging |
| Asym | https://github.com/stnava/asymmetry | asymmetry analysis with ANTs |
| C | https://github.com/stnava/C | "C"lassic large deformation example |
| PTBP | https://github.com/stnava/PediatricTemplateOfBrainPerfusion | analysis in PTBP paper |
| butterfly | https://github.com/stnava/butterfly | multi-start registration example |
| Haxby | https://github.com/stnava/Haxby2001 | reproduce face recognition decoding results (may be out of date but could be revived with small efforts) |
| rfmri | https://github.com/stnava/RfMRI | fmri processing examples in ANTsR (may be out of date but could be revived with small efforts) |
| cars | https://github.com/stnava/cars | an old example mapping between an american and german vehicle |
| antsTut | https://github.com/stnava/ANTsTutorial | evolving tutorial materials |
| visualization | https://github.com/ntustison/antsVisualizationExamples | Examples for ``antsSurf``, ``antsVol``, and ``CreateTiledMosaic``|
| template | https://github.com/ntustison/TemplateBuildingExample | Template building examples (brain and faces) |
| antsCT | https://github.com/ntustison/antsCorticalThicknessExample | 2-D ``antsCorticalThickness.sh`` examples. |
| antsJLF | https://github.com/ntustison/MalfLabelingExample | joint label fusion example. |
| antsBrainExtraction | https://github.com/ntustison/antsBrainExtractionExample | Example for ``antsBrainExtraction.sh`` |
| antsAtroposN4 | https://github.com/ntustison/antsAtroposN4Example | Example for ``antsAtroposN4.sh`` |
| makePriors | https://github.com/ntustison/antsCookTemplatePriorsExample | "Cook" template priors |
| lungReg | https://github.com/ntustison/antsCtLungRegistrationExample | Combine separate left/right lung registrations |
| lobeLungJLF | https://github.com/ntustison/LungAndLobeEstimationExample | Use JLF to estimate lung and lobes |
| LungRegMask | https://github.com/ntustison/ProtonCtLungMaskRegistration | Register lung masks from CT and MRI |