RNiftyReg: Image Registration Using the NiftyReg Library

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Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.

Author
Jon Clayden, based on original code by Marc Modat, Pankaj Daga and others
Date of publication
2016-12-08 15:49:10
Maintainer
Jon Clayden <code@clayden.org>
License
GPL-2
Version
2.4.1
URLs

View on CRAN

Man pages

affine
Create, test for and print affine matrices
applyTransform
Apply a precomputed transformation
buildAffine
Build an affine matrix up from its constituent...
composeTransforms
Compose transformations
decomposeAffine
Decompose an affine matrix into its constituent...
deformationField
Calculate the deformation field for a transformation
forward
Extract forward and reverse transformations
halfTransform
Calculate a half transformation
invertAffine
Invert an affine matrix
isImage
Test whether an object represents an image
jacobian
Extract a Jacobian determinant map
niftyreg
Two and three dimensional image registration
niftyreg.linear
Two and three dimensional linear image registration
niftyreg.nonlinear
Two and three dimensional nonlinear image registration
readAffine
Read an affine matrix from a file
readNifti
Read a NIfTI-1 format file
reexports
Objects exported from other packages
similarity
Similarity measures between images
writeAffine
Write an affine matrix to a file

Files in this package

RNiftyReg
RNiftyReg/inst
RNiftyReg/inst/extdata
RNiftyReg/inst/extdata/flash_t1.nii.gz
RNiftyReg/inst/extdata/mni_brain.nii.gz
RNiftyReg/inst/extdata/house_colour_large.jpg
RNiftyReg/inst/extdata/control.nii.gz
RNiftyReg/inst/extdata/house_colour.png
RNiftyReg/inst/extdata/affine.txt
RNiftyReg/inst/extdata/epi_t2.nii.gz
RNiftyReg/inst/extdata/house.png
RNiftyReg/tests
RNiftyReg/tests/testthat
RNiftyReg/tests/testthat/test-15-affine.R
RNiftyReg/tests/testthat/test-20-niftyreg.R
RNiftyReg/tests/testthat/flirt.mat
RNiftyReg/tests/testthat/test-25-transform.R
RNiftyReg/tests/testthat/test-30-multireg.R
RNiftyReg/tests/test-all.R
RNiftyReg/src
RNiftyReg/src/Makevars
RNiftyReg/src/DeformationField.cpp
RNiftyReg/src/RNifti.cpp
RNiftyReg/src/aladin.cpp
RNiftyReg/src/reg-lib
RNiftyReg/src/reg-lib/Kernels.h
RNiftyReg/src/reg-lib/_reg_aladin_sym.cpp
RNiftyReg/src/reg-lib/AffineDeformationFieldKernel.h
RNiftyReg/src/reg-lib/_reg_aladin.cpp
RNiftyReg/src/reg-lib/cpu
RNiftyReg/src/reg-lib/cpu/_reg_macros.h
RNiftyReg/src/reg-lib/cpu/_reg_globalTrans.cpp
RNiftyReg/src/reg-lib/cpu/_reg_nmi.h
RNiftyReg/src/reg-lib/cpu/CPUKernels.cpp
RNiftyReg/src/reg-lib/cpu/CPUBlockMatchingKernel.h
RNiftyReg/src/reg-lib/cpu/CPUResampleImageKernel.h
RNiftyReg/src/reg-lib/cpu/CPUAffineDeformationFieldKernel.cpp
RNiftyReg/src/reg-lib/cpu/_reg_thinPlateSpline.h
RNiftyReg/src/reg-lib/cpu/CPUConvolutionKernel.h
RNiftyReg/src/reg-lib/cpu/_reg_KLdivergence.h
RNiftyReg/src/reg-lib/cpu/_reg_blockMatching.h
RNiftyReg/src/reg-lib/cpu/CPUOptimiseKernel.h
RNiftyReg/src/reg-lib/cpu/_reg_tools.cpp
RNiftyReg/src/reg-lib/cpu/CPUBlockMatchingKernel.cpp
RNiftyReg/src/reg-lib/cpu/_reg_maths.h
RNiftyReg/src/reg-lib/cpu/_reg_localTrans_jacobian.cpp
RNiftyReg/src/reg-lib/cpu/_reg_localTrans.h
RNiftyReg/src/reg-lib/cpu/_reg_globalTrans.h
RNiftyReg/src/reg-lib/cpu/_reg_KLdivergence.cpp
RNiftyReg/src/reg-lib/cpu/_reg_resampling.cpp
RNiftyReg/src/reg-lib/cpu/_reg_polyAffine.cpp
RNiftyReg/src/reg-lib/cpu/_reg_measure.h
RNiftyReg/src/reg-lib/cpu/CPUOptimiseKernel.cpp
RNiftyReg/src/reg-lib/cpu/_reg_optimiser.h
RNiftyReg/src/reg-lib/cpu/CPUKernels.h
RNiftyReg/src/reg-lib/cpu/CPUKernelFactory.h
RNiftyReg/src/reg-lib/cpu/CPUKernelFactory.cpp
RNiftyReg/src/reg-lib/cpu/_reg_femTrans.cpp
RNiftyReg/src/reg-lib/cpu/CPUConvolutionKernel.cpp
RNiftyReg/src/reg-lib/cpu/_reg_localTrans_regularisation.cpp
RNiftyReg/src/reg-lib/cpu/_reg_maths.cpp
RNiftyReg/src/reg-lib/cpu/_reg_dti.h
RNiftyReg/src/reg-lib/cpu/CPUAffineDeformationFieldKernel.h
RNiftyReg/src/reg-lib/cpu/_reg_ssd.cpp
RNiftyReg/src/reg-lib/cpu/_reg_tools.h
RNiftyReg/src/reg-lib/cpu/_reg_resampling.h
RNiftyReg/src/reg-lib/cpu/_reg_polyAffine.h
RNiftyReg/src/reg-lib/cpu/_reg_blockMatching.cpp
RNiftyReg/src/reg-lib/cpu/_reg_ssd.h
RNiftyReg/src/reg-lib/cpu/CPUResampleImageKernel.cpp
RNiftyReg/src/reg-lib/cpu/_reg_localTrans.cpp
RNiftyReg/src/reg-lib/cpu/_reg_lncc.h
RNiftyReg/src/reg-lib/cpu/_reg_thinPlateSpline.cpp
RNiftyReg/src/reg-lib/cpu/_reg_femTrans.h
RNiftyReg/src/reg-lib/cpu/_reg_lncc.cpp
RNiftyReg/src/reg-lib/cpu/_reg_optimiser.cpp
RNiftyReg/src/reg-lib/cpu/_reg_dti.cpp
RNiftyReg/src/reg-lib/cpu/_reg_nmi.cpp
RNiftyReg/src/reg-lib/Content.h
RNiftyReg/src/reg-lib/_reg_f3d2.cpp
RNiftyReg/src/reg-lib/_reg_polyAffine.cpp
RNiftyReg/src/reg-lib/_reg_base.cpp
RNiftyReg/src/reg-lib/_reg_f3d2.h
RNiftyReg/src/reg-lib/_reg_aladin.h
RNiftyReg/src/reg-lib/_reg_aladin_sym.h
RNiftyReg/src/reg-lib/_reg_f3d_sym.cpp
RNiftyReg/src/reg-lib/OptimiseKernel.h
RNiftyReg/src/reg-lib/_reg_polyAffine.h
RNiftyReg/src/reg-lib/_reg_base.h
RNiftyReg/src/reg-lib/BlockMatchingKernel.h
RNiftyReg/src/reg-lib/Platform.cpp
RNiftyReg/src/reg-lib/ResampleImageKernel.h
RNiftyReg/src/reg-lib/_reg_f3d_sym.h
RNiftyReg/src/reg-lib/Platform.h
RNiftyReg/src/reg-lib/ConvolutionKernel.h
RNiftyReg/src/reg-lib/_reg_f3d.cpp
RNiftyReg/src/reg-lib/Content.cpp
RNiftyReg/src/reg-lib/_reg_f3d.h
RNiftyReg/src/reg-lib/Kernel.h
RNiftyReg/src/reg-lib/KernelFactory.h
RNiftyReg/src/config.h
RNiftyReg/src/AffineMatrix.h
RNiftyReg/src/DeformationField.h
RNiftyReg/src/main.cpp
RNiftyReg/src/f3d.h
RNiftyReg/src/aladin.h
RNiftyReg/src/AffineMatrix.cpp
RNiftyReg/src/f3d.cpp
RNiftyReg/NAMESPACE
RNiftyReg/NEWS
RNiftyReg/R
RNiftyReg/R/affine.R
RNiftyReg/R/niftyreg.R
RNiftyReg/R/nifti.R
RNiftyReg/R/image.R
RNiftyReg/R/transform.R
RNiftyReg/R/zzz.R
RNiftyReg/README.md
RNiftyReg/MD5
RNiftyReg/DESCRIPTION
RNiftyReg/man
RNiftyReg/man/applyTransform.Rd
RNiftyReg/man/composeTransforms.Rd
RNiftyReg/man/forward.Rd
RNiftyReg/man/isImage.Rd
RNiftyReg/man/deformationField.Rd
RNiftyReg/man/decomposeAffine.Rd
RNiftyReg/man/niftyreg.nonlinear.Rd
RNiftyReg/man/readNifti.Rd
RNiftyReg/man/writeAffine.Rd
RNiftyReg/man/similarity.Rd
RNiftyReg/man/jacobian.Rd
RNiftyReg/man/halfTransform.Rd
RNiftyReg/man/affine.Rd
RNiftyReg/man/niftyreg.Rd
RNiftyReg/man/reexports.Rd
RNiftyReg/man/readAffine.Rd
RNiftyReg/man/invertAffine.Rd
RNiftyReg/man/niftyreg.linear.Rd
RNiftyReg/man/buildAffine.Rd