Significant changes to the RNiftyReg package are laid out below for each release.

=================================================================================

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.

=================================================================================
