This release contains a bug fix for the previous bug fix - antsApplyTransforms was not outputting tensor data at all, and instead produced a blank image.

Also fix a bug that affects file backups for template construction - doesn't affect the processing itself.

Thanks to @Mazhe123 for reporting the tensor bug. Apologies for the inconvenience.

What's Changed

• BUG: Backup templates tried to copy non-existent files by @cookpa in #1890
• BUG: Need to compute Exp(D) before reorienting by @cookpa in #1892

Full Changelog: v2.6.1...v2.6.2

This is a bug fix release with important changes to Jacobian estimation and tensor reorientation.

See #1884 for Jacobians and #1880 for tensors. Please open an issue or discussion if there are any questions.

What's Changed

• BUG: Fix tensor reorientation with displacement fields by @cookpa in #1871
• ENH: Support composite transforms in ReorientTensorImage by @cookpa in #1874
• Dt background value by @cookpa in #1875
• Apply PPD reorientation for tensor data in antsApplyTransforms by @cookpa in #1879
• ENH: Allow writing Jacobian matrix as NIFTI by @cookpa in #1885
• BUG: Jacobian determinants incorrect for non-identity direction matrices by @cookpa in #1887

Full Changelog: v2.6.0...v2.6.1

This version is built with ITK 5.4.3.

Registration

• Improvements to "syn only" transforms in antsRegistrationSyN*.sh scripts: these scripts now assume an identity initial transform, rather than doing a center-of-mass alignment by default. This better serves the usual use case for these kinds of transforms, either correcting nonlinear distortions in images from the same session, or doing nonlinear registration on images that have already been rigidly aligned.

• The default CC radius and update step size in antsRegistrationSyN*.sh` have changed. Based on evaluations by @ntustison, a CC radius of 2 voxels is preferable to 4. The default step size of 0.1 in SyN registration has been increased to 0.2. Both of these can still be controlled by the user on the command line.

• Histogram matching has been turned off by default in antsCorticalThickness.sh and the antsMultivariateTemplateConstruction*.sh scripts. It was already off by default in antsRegistrationSyN*.sh. An improved histogram matching function has been added to ANTsPy. If histogram matching is required, we recommend doing it as a preprocessing step so that it can be checked and done with the appropriate masks.

• Composite transforms can now be written directly from antsApplyTransforms, without having to call CompositeTransformUtil.

• An optimizer bug that could lead to unpredictable and suboptimal results in antsAI has been fixed.

Other fixes

• Remove median computation for scalar images in LabelGeometryMeasures, because the filter uses a median approximation that can be inaccurate for some data (eg, statistical maps).

• A very longstanding bug in CreateTiledMosaic is fixed: it will now output a tiled image without an RGB overlay. The overlay was supposed to be optional but was in fact required.

• Handle windows newlines (used in Python CSV files on all platforms) in template construction input - this avoids confusing errors when passing CSV files as input to the template scripts.

Distribution

CentOS 7 binaries are back, Ubuntu 20.04 moved to docker build.

Thanks to all contributors of code, bug reports, test data, and other help.

What's Changed

• ENH: identity init transform for (bspline)syn-only by @cookpa in #1817
• ENH: Make COM translation consistent with antsRegistration by @cookpa in #1821
• ENH: Enhanced error checking by @cookpa in #1822
• ENH: Change radius and gradient step defaults. by @ntustison in #1829
• STYLE: Add itkVirtualGetNameOfClassMacro + itkOverrideGetNameOfClassMacro by @hjmjohnson in #1832
• replace itkstaticconstmacro with constexpr by @hjmjohnson in #1833
• ENH: Update default gradient step, turn off histogram matching by @cookpa in #1831
• ENH: Check dimensionality of input warp fields. by @cookpa in #1835
• DOC: Link to conda forge by @cookpa in #1837
• ENH: use prefix of 1st param from --output for --write-interval-volumes by @mathdugre in #1838
• Write composite transforms from antsApplyTransforms by @cookpa in #1839
• ENH: use prefix from --output for --write-interval-volumes by @mathdugre in #1840
• DOC: Better usage by @cookpa in #1841
• ENH: Strip carriage returns from template input by @cookpa in #1845
• CI: Move ubuntu 20.04 to Docker, revive Centos7 by @cookpa in #1846
• ENH: Update ITK tag. by @ntustison in #1847
• BUG: CreateTiledMosaic would not write images without an RGB overlay by @cookpa in #1849
• ENH: Remove static output stream that was causing problems with ANTsPy by @cookpa in #1851
• Label geometry histogram by @cookpa in #1854
• BUG: Set scales estimator for antsAI by @cookpa in #1861
• ENH: Update itk release by @cookpa in #1865

New Contributors

• @mathdugre made their first contribution in #1838

Full Changelog: v2.5.4...v2.6.0

One main bug fix for Atropos, which had an overflow bug affecting large images.

Main new feature is the ability of antsApplyTransforms to apply transforms to individual volumes of a time series. This makes it easier to apply time-varying transforms (like motion correction) sequentially without decomposing the time series into individual volumes.

There's also updates to the release binaries: MacOS 12 runners are being removed by Github, so Intel Mac binaries are moving to MacOS 13. The Linux releases will now include Alma Linux 8 and 9.

What's Changed

• DOC: Fix wrong link for ANTsPy in README by @NicolasGensollen in #1781
• ENH: CI updates by @cookpa in #1783
• BUG: Fix script usage by @cookpa in #1785
• BUG: float type for posterior sum caused overflow on large images by @cookpa in #1793
• DOC: Usage, --write-displacement 0 by @cookpa in #1798
• DOC: Clarify -a usage by @cookpa in #1799
• ENH: apply transform to single slice of time series by @cookpa in #1800
• ENH: More image read checks by @cookpa in #1807
• CI: Update macos to 13 by @cookpa in #1810
• CI: Fix artifact names by @cookpa in #1811
• CI: Add alma9 to releases by @cookpa in #1813

New Contributors

• @NicolasGensollen made their first contribution in #1781

Full Changelog: v2.5.3...v2.5.4

New capabilities in antsTransformInfo to print affine jacobian determinants. Also fixes for Atropos and template construction with antsMultivariateTemplateConstruction2.sh.

What's Changed

• CI: Docker tags by @cookpa in #1748
• ENH: Add Ubuntu 24.04 by @gdevenyi in #1751
• ENH: update and reformat README by @ncullen93 in #1750
• DOC: Create CITATION.cff by @cookpa in #1752
• Refactor antsTransformInfo to add some error handling and compute determinant by @gdevenyi in #1712
• BUG: Manifold parzen windows. by @ntustison in #1757
• BUG: intermediate template file names by @cookpa in #1762
• BUG: Address degenerate case. by @ntustison in #1767
• ENH: write template output such that things sort together by @cookpa in #1771
• BUG: Fix release tags by @cookpa in #1776
• BUG: fixing tags again by @cookpa in #1778
• BUG: VAR=0; ((VAR++)) fails on Linux but not on Mac by @cookpa in #1779

Full Changelog: v2.5.2...v2.5.3

The main change here is LabelGeometryMeasures, which has been updated to use a new filter. The previous filter is set to be deprecated by ITK because of computational inefficiencies and bugs, see InsightSoftwareConsortium/ITK#4630.

What's Changed

• COMP: Address warnings. by @ntustison in #1669
• COMP: More warnings. by @ntustison in #1670
• DOC: MI clarification in logger. by @ntustison in #1671
• COMP: ANTs warnings 3. by @ntustison in #1672
• ENH: Use new M1 runner by @cookpa in #1673
• ENH: Update ITK to incorporate faster point set checks by @cookpa in #1676
• ENH: Support averaging affine transforms with float parameters by @dzenanz in #1682
• Refactor AverageAffineTransformFunction by @dzenanz in #1684
• ENH: Retain docker image from PRs by @cookpa in #1685
• COMP: Update actions to avoid node deprecation warnings by @cookpa in #1686
• ENH: Display debugging parameters only when verbose flag is turned on by @dzenanz in #1690
• ENH/BUG: CompositeTransformUtil --disassemble prepended to the output… by @cookpa in #1695
• BUG: Need to fill buffer for R and Python interfaces. by @ntustison in #1699
• ENH: Check for initialization after image allocation. by @ntustison in #1702
• ENH: Suppress "Bad Rotation Matrix" warnings by @dzenanz in #1697
• BUG: KellyKapowski could not infer dimensionality from input by @cookpa in #1698
• COMP: Cancel previous ci builds by @cookpa in #1705
• ENH: Check input for antsApplyTransforms matches dimensionality by @cookpa in #1694
• BUG: iMath Truncate failed on images with negative intensities by @cookpa in #1710
• ENH: make lesion image uint16 to allow more than 255 lesions by @cookpa in #1716
• Fix hardcoded dimension in template construction by @mabulnaga in #1719
• ENH: Add dimension 4. by @ntustison in #1722
• Use structured form for tech support requests by @cookpa in #1729
• CI: Drop v from release versions by @cookpa in #1732
• ENH: More than 10 modalities. by @ntustison in #1739
• COMP: Remove warnings. by @ntustison in #1740
• ENH: Update LabelGeometryMeasures to not use deprecated filter by @cookpa in #1737
• Remove deprecated label geometry filter by @cookpa in #1741
• ENH: Make eccentricity more similar to elongation by @cookpa in #1743

New Contributors

• @mabulnaga made their first contribution in #1719

Full Changelog: v2.5.1...v2.5.2

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

• ENH: Remove system zlib from container by @cookpa in #1592
• COMP: Github windows runners were attempting to use deprecated by @cookpa in #1594
• COMP: need to import random by @cookpa in #1596
• BUG: check for required programs by @cookpa in #1600
• ENH: Allow priors to be specified with BIDS labels in ants*CorticalThickness.sh by @cookpa in #1604
• ENH: Clarify usage and catch missing ImageDimension by @cookpa in #1619
• ENH: Expose forward/inverse cumulative velocity fields. by @ntustison in #1630
• BUG: Template input overwritten when basename identical by @cookpa in #1635
• ENH: Better to use actual index into imageset array by @cookpa in #1636
• Make antsBrainExtraction.sh less sensitive to image size by @cookpa in #1640
• COMP: Fix some compile errors when legacy functionality is removed by @dzenanz in #1650
• A variety of compile fixes which appear when legacy is disabled by @dzenanz in #1651
• COMP: Avoid type conversion errors on Mac with new ITK by @cookpa in #1659
• COMP: Fix compile warning C4858: discarding return value in std::remove by @dzenanz in #1660
• COMP: Add missing include headers by @dzenanz in #1661
• COMP: Fix some CMake warnings by @cookpa in #1662
• ENH: Install cmake using apt by @jennydaman in #1647
• BUG: Stop segmentation fault when Atropos is multi-threaded by @cookpa in #1663
• ENH: Allow static libs, re-enable testing by @cookpa in #1665

New Contributors

• @dzenanz made their first contribution in #1650
• @jennydaman made their first contribution in #1647

Full Changelog: v2.5.0...v2.5.1

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

• ENH: Add Ubuntu 18.04 builds via docker by @cookpa in #1533
• COMP: Workflow for tracking github traffic by @cookpa in #1534
• BUG: antsAI exception with < 10 start points by @cookpa in #1539
• ANTsCT random seed by @cookpa in #1541
• COMP: Address some compilation warnings. by @ntustison in #1542
• DOC: Update license to Apache 2.0 by @cookpa in #1548
• WIP: Add CONTRIBUTING.md by @cookpa in #1549
• BUG: Fix typos by @cookpa in #1552
• BUG: Wrong elapsed time in registration stage by @cookpa in #1554
• BUG: Wrong return type. by @ntustison in #1562
• ENH: Add spacing option for laplacian sharpening. by @ntustison in #1543
• ENH: Update ITK git tag. by @ntustison in #1566
• BUG: Avoid composite transform mangling. by @ntustison in #1567
• ENH: exit with error if registration shrink factors, convergence, smo… by @cookpa in #1571
• BUG: Avoid divide by 0. by @ntustison in #1575
• Remove ANTSPATH by @ghisvail in #1574
• BUG: DenoiseImage check by @cookpa in #1577
• ENH: Fix output dir logic in scripts, check dim in template construction by @cookpa in #1578
• Fix: don't repeat N4 every iteration by @gdevenyi in #1591

Full Changelog: v2.4.4...v2.5.0

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

• BUG: Bump ITK to fix random seeding for SyN by @cookpa in #1478
• ENH: Use ITK ZLIB, test release builds, Windows binaries (#1) by @cookpa in #1484
• COMP: Update actions to resolve deprecation warnings by @cookpa in #1485
• COMP: Update docker login action by @cookpa in #1486
• SVN → Git by @DimitriPapadopoulos in #1506
• ENH: Read Windows pointers by @cookpa in #1513
• BUG: Was counting newline in windows pointer string test by @cookpa in #1515
• ENH: Parse windows pointers for write operations [skip ci] by @cookpa in #1516
• Do not prepend v to version by @DimitriPapadopoulos in #1504
• Clarify antsBrainExtraction.sh usage by @cookpa in #1520
• Enable MINC support by default by @gdevenyi in #1526
• ENH: Clarify usage, skip intensity image if it is "none" or "na" by @cookpa in #1530
• DOC: Recommend Mattes MI as the default metric by @cookpa in #1531
• BUG: Enable sparse sampling of metrics in SyN registration by @ntustison in 14e7312

New Contributors

• @DimitriPapadopoulos made their first contribution in #1506

Full Changelog: v2.4.3...v2.4.4

This version is configured to build with ITK 5.3.0.

What's Changed

• BUG: Remove hard-coded lib dir that was breaking centos builds by @cookpa in #1434
• ENH: Check AverageImages input files can be read by @cookpa in #1436
• COMP: Pass optimization flags to ITK and ANTS-build by @cookpa in #1445
• ENH: Install scripts for non-release configurations by @cookpa in #1449
• ENH: antsAtroposN4.sh - exposed more subcommand parameters as arguments by @br-cpvc in #1420
• STYLE: Clarify usage of antsAtroposN4.sh and make defaults visible by @cookpa in #1450
• BUG: Atropos no longer segfaults when -i is missing, it reports an error msg instead by @br-cpvc in #1454
• PERF: Bump ITK to control multi-threading in MI registration. by @cookpa in #1455
• BUG: fixed Scripts/antsAtroposN4.sh not stopping when subcommands exit with exitcode>0 by @br-cpvc in #1456
• BUG: Needed to exit immediately if mask is missing by @cookpa in #1458
• BUG: Need the slash on ANTSPATH by @cookpa in #1457
• PERF: accelerating antsAtroposSegmentationImageFilter.hxx function GetPosteriorProbabilityImage using ITK ParallelizeImageRegion by @br-cpvc in #1462
• ENH: Make "-u" option also set a random seed for registration by @cookpa in #1468
• BUG: Set sampling percentage and strategy for SyN by @ntustison in 14e7312
• ENH: Set ITK version to 5.3.0 by @cookpa in #1477

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: v2.4.2...v2.4.3