Advanced Normalization Tools uses github to organize and distribute simple, reproducible examples. We also provide a wiki and the indispensable antsHandout. We also perform tutorials when invited to do so.
| 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 illustrates several use cases throughout its vignettes and documentation. 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 will also be a source of help.
These are different than wiki examples in that they come with data.
A user interested in these examples should clone the repository via git.
git clone reponame.gitThe 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 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 |