[R-pkgs] Significant updates to medical imaging packages: TractoR and RNiftyReg

Jon Clayden jon.clayden at gmail.com
Thu Apr 12 00:22:54 CEST 2012

Dear all,

There have been some recent major updates to the TractoR and RNiftyReg
packages, which are available for medical image analysis applications.
If you use R for these purposes, I hope you will find the updates

RNiftyReg is an image registration package, which provides a clean
R-like interface to the NiftyReg library developed at University
College London [1]. It is aimed at medical image registration, but
could be applied to 2D or 3D coalignment of images of any type.
RNiftyReg version 0.6 adds an interface to the NiftyReg nonlinear
registration tool "f3d", which performs fast freeform
deformation-based registration based on a grid of control points. This
is a fast implementation, which can perform 3D registration in under a
minute for some medical images. The package is on CRAN, and
development is coordinated through GitHub [2].

TractoR is a larger project for medical image analysis, particularly
with magnetic resonance images [3]. It provides tools for reading,
writing, visualising, manipulating and processing MR images in R. The
tractor.base package is on CRAN, and forms the backbone of the
project. Significant additions to this package in the 2.x series of
releases include:

- Extensive use of the reference classes introduced in R 2.12.0.
- Coercion methods between TractoR's "MriImage" class and the "nifti"
class in the oro.nifti package.
- Specific support for sparse images (of any dimensionality).
- The ability to read and write the MGH file format used by the
Freesurfer software package.
- A substantial number of other functionality and performance
improvements, as well as bug fixes.

The full TractoR distribution includes four other R packages, each
somewhat more specialised than tractor.base, as well as a flexible
command-line interface which can be used to perform common tasks
quickly. Details can be found in a recent JSS paper on TractoR [4].

All the best,

[1] http://sourceforge.net/projects/niftyreg/
[2] https://github.com/jonclayden/RNiftyReg
[3] http://www.tractor-mri.org.uk
[4] http://www.jstatsoft.org/v44/i08/

Jonathan D Clayden, PhD
Lecturer in Neuroimaging and Biophysics
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street
United Kingdom

t | +44 (0)20 7905 2708
f | +44 (0)20 7905 2358
w | www.homepages.ucl.ac.uk/~sejjjd2/
w | www.diffusion-mri.org.uk/people/1

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