ANTsX ANTs Versions Save

Advanced Normalization Tools (ANTs)

v2.5.1

3 months ago

This release fixes a bug that caused Atropos to fail when using the HistogramParzenWindows likelihood model with multiple threads.

Script fixes and updates include better support for different head sizes in antsBrainExtraction.sh, and support for priors in BIDS format in antsCorticalThickness.sh.

The docker image is also updated (thanks @jennydaman) for improved performance and compatibility with different hardware architectures.

Update: added binaries for Apple Silicon with Mac OS 14.

What's Changed

New Contributors

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.5.0...v2.5.1

v2.5.0

8 months ago

ANTSPATH is no longer required for ANTs scripts. We now defer to PATH for ANTs binaries and scripts. Thanks to @ghisvail for this fix.

What's Changed

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.4.4...v2.5.0

v2.4.4

1 year ago

Mostly computational updates, the big one is the addition of Windows binaries. Links to PRs below. Some highlights

  • Windows binaries are built on the Github runner with Windows Server 2022, Visual Studio 2019. This is the first Windows release in some time, so please share feedback via issues or discussions.
  • Use ITK's ZLIB library, which means users will no longer need to install system zlib to build ANTs.
  • MINC support is turned on by default, so that ANTs will be able to use MINC I/O without needing to build with special options. That means binaries attached to this release will support MINC.

What's Changed

New Contributors

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.4.3...v2.4.4

v2.4.3

1 year ago

This version is configured to build with ITK 5.3.0.

What's Changed

Note about the sampling strategy in SyN: this release allows sparse metric sampling in SyN, eg you can use Regular or Random sampling in the metric. Previously, these options were silently ignored for SyN (but not for other transforms). However, user-defined random seeds are not used in SyN and BSplineSyN. Fixing this required an ITK change and will be resolved in the next release. The default in all ANTs scripts is to use dense sampling in SyN / BSplineSyN, which are not affected.

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.4.2...v2.4.3

v2.4.2

1 year ago

What's Changed

  • BUG: Fix bug causing antsRegistration to fail unless --float was used
  • Incorporate ITK performance optimization for b-spline estimation (see #1017, thanks @ntustison , @chrisadamsonmcri and others)
  • ENH: graceful exit Atropos in case of non-existing input files by @br-cpvc in https://github.com/ANTsX/ANTs/pull/1422
  • DOC: added missing end parenthesis to Atropos documentation string by @br-cpvc in https://github.com/ANTsX/ANTs/pull/1421

New Contributors

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.4.1...v2.4.2

v2.4.1

1 year ago

What's Changed

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.4.0...v2.4.1

v2.4.0

1 year ago

Highlights (see full list of PRs below)

Bug fixes:

  • Fix Docker container bug affecting antsAtroposN4 convergence (#1334).
  • Fix ImageMath function ExtractComponentFrom3DTensor.
  • Multiple fixes to template construction scripts. Do not fall back on population average if initial template is specified but the file is not found. Check that all input images are successfully registered and that template updates complete successfully at each iteration.
  • Fix template prior cooking bug causing priors to be zeroed out due to precision errors.
  • Fix LesionFilling divide by zero error (#1258)
  • Fix bug in joint label fusion affecting multi-modality atlases (#1302)
  • Fix exception in PrintHeader spatial orientation reporting (#1382)
  • Denoise all inputs to antsAtroposN4.sh, and remove duplicate denoising steps to save time (#1373)

New features:

  • Option to pass an initial affine transform to antsBrainExtraction.sh.
  • Option to control SyN gradient steps in antsRegistrationSyN scripts.
  • Reproducible multi-threaded registration options (#1190)
  • Multiple updates to template building scripts. New options to control template averaging and sharpening, and make unbiased initialization more robust. Store intermediate templates after each iteration so that users can assess convergence and if needed, re-use previous templates for a new run of the script.
  • Kinematics tensors in ImageMath.
  • Support transforms of AFNI 5D statistical images.
  • Write HDF5 ITK transform objects with antsApplyTransforms (#1317).
  • Add gradient filter smoothing options to improve metric stability (#1351)
  • Allow smoothing in antsMotionCorr to have mm or vox units, change defaults to vox for consistency with antsRegistration (#1350).

Code and documentation:

  • Clarify behavior of N4 rescaling option.
  • Updates to template and cortical thickness script usage.
  • Improved VNL vector and matrix implementation.
  • Update code for C++14.
  • Add compilation support for IBM POWER architectures (#1243)
  • Update version information so that source tarballs contain a correct version number.
  • Move Docker CI build to Github Actions
  • Run short tests during Docker CI build (#1365).
  • Remove support for deprecated git protocol
  • Update ITK

What's Changed

New Contributors

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.3.5...v2.4.0

v2.3.5

3 years ago

Update 2022-04-23: Github has disabled the unencrypted git:// protocol. To compile this and previous releases as superbuilds, you must set the Git protocol to https with the cmake option ANTS_USE_GIT_PROTOCOL to OFF.

Bug fixes:

  • Fix an error in the multi-resolution framework of ANTS. This affects registration quality in ANTS and antsMultivariateTemplateConstruction.sh, but antsRegistration / antsCorticalThickness.sh / antsMultivariateTemplateConstruction2.sh were not affected.
  • Fix for building ANTs with code style checking.
  • Removed outdated server addresses for test data.
  • Fix resolution for QC PNG images in antsCorticalThickness.sh.
  • Allow antsSliceRegularizedRegistration to run with zero regularization.

New features:

  • Incorporate ITK update that uses NIFTI sform transforms where possible, reducing precision errors in header orientation. More details at this ANTs Wiki page.
  • Added additional features to N3, with updated user interface.
  • Harmonized cortical thickness default parameters (for KellyKapowski) across all ANTsX software.

Code and documentation:

  • Various code fixes to resolve warnings and improve ITK compatibility.
  • Added code of conduct for ANTs community.
  • Clarify usage of antsRegistration.
  • Include ITK implementation of adaptive denoising.
  • ANTs Docker image on DockerHub only updates from the the master branch, rather than any branch / pull request.

v2.3.4

3 years ago

New features:

  • AddNoiseToImage
  • Unsharp mask filter added to ImageMath
  • Additional output data type options for antsApplyTransforms
  • Option to install libraries only for more compact ANTsR builds

Bug fixes:

  • N4BiasFieldCorrection
  • ImageMath (morphological operators)
  • Bug fixes for ImageMath morphological operators
  • Command line arg bug fixes and improvements for N3BiasFieldCorrection, antsRegistration, antsApplyTransforms, antsMotionCorr

Code and documentation:

  • Multiple code updates for C++11
  • Documentation of none sampling strategy in antsSliceRegularizedRegistration
  • ITKv5 compatibility
  • CMake improvements for containers, multi-platform compatibility

v2.3.3

3 years ago

This release contains a bug in antsRegistrationSyN.sh that is fixed in the 2.3.4 release.

  • n4 bug fixes
  • Unsharp mask filter added to ImageMath
  • Bug fixes for ImageMath morphological operators
  • Command line arg bug fixes and improvements for N3BiasFieldCorrection, antsRegistration, antsApplyTransforms, antsMotionCorr
  • Option to install libraries only for more compact ANTsR builds
  • Multiple code updates for C++11
  • DOC: none sampling strategy
  • ITKv5 compatibility
  • cmake improvements for containers, distribution, etc