Significant changes to the RNiftyReg package are laid out below for each release.
=================================================================================
VERSION 2.0.1
- Fixes for Solaris compilation and UBSAN issues.
=================================================================================
VERSION 2.0.0
- This is a more-or-less complete rewrite of the package, with the goals of
simplifying both the package's dependencies and its usage. The upstream
NiftyReg code has also been updated. However, it should still be possible to
read and use transformations created using RNiftyReg 1.x.
- The oro.nifti package is no longer needed, nor used for reading and writing
NIfTI files (RNiftyReg now offers readNifti() and writeNifti(), which are much
faster). However, objects of S4 class "nifti" can still be used with the
package if desired. Functions return either plain R arrays with attributes, or
bare-bones "internalImage" objects, which contain only some basic metadata and
a pointer to a C-level data structure.
- There are new functions for halving a transform (halfTransform), composing two
transforms (composeTransforms), and building an affine transform from scratch
(buildAffine).
- Registration is now symmetric by default (for both linear and nonlinear), a
newer symmetric nonlinear approach is now used, and default cost function
weights have been tweaked. Therefore, the arguments to the core niftyreg()
function, and its linear and nonlinear special cases, have changed in both name
and defaults. See ?niftyreg and related help pages for details.
- It is no longer necessary to use functions specific to transform type to
perform many operations. For example, the work of the old applyAffine(),
applyControlPoints(), transformWithAffine() and transformWithControlPoints()
functions is done by the flexible new applyTransform() function. The forward
and reverse transforms can always be obtained from a registration using the new
forward() and reverse() functions, no matter what their type is. However, some
affine-only functions, such as decomposeAffine(), retain their names.
- The "affineType" attribute has gone, and convertAffine() is no longer a
user-visible function. All affine matrices are stored using the NiftyReg
convention. FSL-FLIRT affines can still be read in, but they are converted to
NiftyReg convention immediately. In addition, source and target image
information is attached to the transforms in attributes, and so does not need
to be specified in most function calls.
- Many smaller changes. The newly updated README file should be used as the main
reference point for usage, supplemented by the R-level function documentation.
=================================================================================
VERSION 1.1.4
- The package was not consistent about how to treat images without NIfTI
orientation information, and this could lead to erroneous results when
transforming points between spaces using an affine matrix. This has been
corrected. (Reported by Jiří Borovec.)
=================================================================================
VERSION 1.1.3
- The C++ code is now more careful to avoid buffer overruns when text fields in
a "nifti" object are too long.
=================================================================================
VERSION 1.1.2
- Some sample data has been added to the package, along with some code examples.
- Code tweaks have been made for C++11 compatibility.
=================================================================================
VERSION 1.1.1
- Under certain circumstances the NiftyReg C++ code could create a control point
image corresponding to an invalid "nifti" object, resulting in a spurious
error when running niftyreg.nonlinear(). This has been corrected. (Reported by
Andreas Heindl.)
=================================================================================
VERSION 1.1.0
- A set of functions has been added for transforming points between spaces using
an affine or nonlinear transformation.
- All registration functions gain an "estimateOnly" option, which can be used to
estimate a transformation without actually resampling the image.
- The new getDeformationField() function can be used to obtain the deformation
field and/or Jacobian determinant map corresponding to a transformation.
- The invertAffine() function has been added to invert an affine matrix while
preserving its "affineType" attribute.
- RNiftyReg will now use OpenMP, if supported by the current build of R.
- Image arguments are now coerced automatically to the "nifti" class if they are
not already of this type.
- Image data is no longer copied between data structure types when not needed,
saving a bit of time and memory.
- It is no longer an error in readAffine() if the affine type is not specified
or stored.
=================================================================================
VERSION 1.0.2
- A further compiler-sensitive problem, which was causing the package to fail to
install using Solaris Studio, has been addressed.
=================================================================================
VERSION 1.0.1
- A Windows-specific compile-time problem has been addressed.
=================================================================================
VERSION 1.0.0
- RNiftyReg now provides an interface to the symmetric version of the NiftyReg
nonlinear registration algorithm. This allows consistent transformations to be
obtained in both directions, in one operation.
- The upstream code has been updated to match NiftyReg v1.3.9. Default cost
function weightings have also been tweaked to match those used in that release.
- The type of an affine matrix is now written to file with it. The type therefore
does not necessarily need to be specified when reading the matrix back in.
- The "interpolationPrecision" option has been removed where it appeared. The
code now simply makes an appropriate choice in each case.
- Internal calculation of the final control point spacing from an initial control
point image was sometimes wrong. This has been corrected.
=================================================================================
VERSION 0.6.2
- Nonlinear registration now works properly for 2D target images.
- Control point spacing is now set from the initial control point image (as it
should be), if one is supplied.
- Two small bugs in the upstream NiftyReg code have been fixed.
- Attempting to perform 4D-to-2D registration now produces a more specific
error message.
=================================================================================
VERSION 0.6.1
- The package now redefines standard C print functions to avoid problems with
output not being captured by R.
=================================================================================
VERSION 0.6.0
- RNiftyReg can now perform nonlinear registration via the niftyreg.nonlinear()
function. This method optimises over a set of moveable control points arranged
in a grid over the image. The applyControlPoints() function has also been
added as the nonlinear equivalent of applyAffine(). See ?niftyreg.nonlinear
for details on these new functions. The niftyreg() function now serves as a
common interface to both the linear and nonlinear optimisations.
- The "initAffine" argument to niftyreg() now accepts a list of matrices as well
as a single affine matrix.
- The upstream NiftyReg code has been updated, thereby taking in a number of
tweaks added since the last release version.
- A bug in the quaternion-to-matrix conversion in xformToAffine() has been fixed.
=================================================================================
VERSION 0.5.0
- The niftyreg() and applyAffine() functions gain an "interpolationPrecision"
argument, which affects the data type of the final image. See ?niftyreg for
details.
- The actual number of algorithm iterations run at each level is now stored in
the output produced by niftyreg().
- A bug has been addressed whereby niftyreg() returned the affine matrix used
for initialisation, if specified, rather than the final one. (Reported by
Brandon Whitcher.)
- The first level of the algorithm is supposed to include both a rigid-body and
affine optimisation, but the latter was previously omitted due to a bug. This
has been corrected. In addition, the first level is allowed twice as many
iterations as subsequent levels, as in the original NiftyReg implementation.
- The "data_type" slot of the "nifti" class is now properly set in the image
returned by niftyreg().
- The underlying NIfTI reference library files have been updated.
- Spurious parameters have been removed to avoid warnings at compile time.
- Calls to problematic C/C++ functions such as exit() have been avoided
(although NIfTI and NiftyReg library functions still use printf() and the
like).
=================================================================================
VERSION 0.4.1
- The reportr package is now properly imported in the namespace file.
=================================================================================
VERSION 0.4.0
- The applyAffine() function has been added as a convenience wrapper to
niftyreg(...,nLevels=0), for applying a precomputed affine transformation to
a new image without further optimisation.
- RNiftyReg now uses the reportr package for message and error reporting.
- The package now has a formal namespace.
=================================================================================
VERSION 0.3.1
- A bug in previous releases affecting the downsampling of images during early
"levels" of alignment has been fixed. Coregistration of larger images, in
particular, should be improved as a result.
=================================================================================
VERSION 0.3.0
- 2D-to-2D, 3D-to-2D and 4D-to-3D registration are now supported by niftyreg().
As a result of this added flexibility, a list of affine matrices, rather than
a single matrix, is now returned by this function.
- An image of fewer than 4 pixels/voxels in any dimension cannot be registered
since it cannot accommodate a single matching block. Providing such an image
as the source or target now produces an error rather than a crash. (Thanks to
Takeo Katsuki for pointing this out.)
- Further documentation improvements.
=================================================================================
VERSION 0.2.0
- Added an option to niftyreg() to control the type of interpolation that is
applied to the final coregistered image.
- Performing better type checking of image data before passing it to the C++
code, to avoid intermittent errors from R.
- Documentation improvements.
=================================================================================
VERSION 0.1.0
- First public release. 3D affine and rigid-body registration are available.
=================================================================================