https://github.com/jefferis/nat.ants

Bridge neuroanatomy toolbox ('nat') and 'ANTs' registration tools
https://github.com/jefferis/nat.ants

image-registration itk neuroanatomy-toolbox r r-package

Last synced: 27 days ago
JSON representation

Bridge neuroanatomy toolbox ('nat') and 'ANTs' registration tools

• Host: GitHub
• URL: https://github.com/jefferis/nat.ants
• Owner: jefferis
• Created: 2018-12-24T00:31:51.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-11-24T00:14:40.000Z (12 months ago)
• Last Synced: 2023-11-24T01:27:04.525Z (12 months ago)
• Topics: image-registration, itk, neuroanatomy-toolbox, r, r-package
• Language: R
• Size: 10.7 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# nat.ants

The goal of nat.ants is to provide a bridge between the [NeuroAnatomy Toolbox](https://jefferis.github.io/nat/)

suite of 3D analysis and visualisation tools for R and the [ANTs](http://stnava.github.io/ANTs/)

image registration toolkit. This is achieved by wrapping the [ANTsRCore](https://github.com/ANTsX/ANTsRCore) 

R package with a small number of functions to enable `nat` functions to use

`ANTs` registrations.

## Installation

ANTsRcore provides everything that you need to use ANTs transformations. This can

make installation a little complicated since it requires compilation of several

large libraries including ITK. The easiest way that we have found to install ANTsRcore

is to use the [neuroconductor project](https://www.neuroconductor.org/package/ANTsRCore).

``` r

source("https://neuroconductor.org/neurocLite.R")

neuro_install('ANTsRCore')

```

You can then install *nat.ants* from GitHub

``` r

# install devtools if required

if (!requireNamespace("devtools")) install.packages("devtools")

# then install nat

devtools::install_github("jefferis/nat.ants")

```

## Example

This example makes use of ANTs registations developed by John Bogovic

and Stephan Saalfeld to map between different Drosophila brains.

See https://www.janelia.org/open-science/jrc-2018-brain-templates for downloads

and further information.

``` r

inv=antsreg("JRC2018F_FAFB/JRC2018F_FAFB1InverseWarp_down.nii.gz",

    "JRC2018F_FAFB/JRC2018F_FAFB0GenericAffine.mat", swap=c(FALSE,TRUE))

fwd=antsreg("JRC2018F_FAFB/JRC2018F_FAFB0GenericAffine.mat",

    "JRC2018F_FAFB/JRC2018F_FAFB1Warp_down.nii.gz", swap=c(TRUE,TRUE))

    

# position of DA1 glomerulus in FAFB

da1glomr.fafb <- cbind(429316, 217924, 42960)

da1glomr.fafbum=da1glomr.fafb/1e3

# map position from FAFB to JRC2018

res <- xform(da1glomr.fafbum, inv)

# and back again

res2 <- xform(res, fwd)

# print out locations

da1glomr.fafbum

res

res2

```