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Recent Releases of ants

ants - Linepithema

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 https://github.com/ANTsX/ANTs/pull/1890
  • BUG: Need to compute Exp(D) before reorienting by @cookpa in https://github.com/ANTsX/ANTs/pull/1892

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.6.1...v2.6.2

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Published by cookpa 9 months ago

ants - Leptomyrmula

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 https://github.com/ANTsX/ANTs/pull/1871
  • ENH: Support composite transforms in ReorientTensorImage by @cookpa in https://github.com/ANTsX/ANTs/pull/1874
  • Dt background value by @cookpa in https://github.com/ANTsX/ANTs/pull/1875
  • Apply PPD reorientation for tensor data in antsApplyTransforms by @cookpa in https://github.com/ANTsX/ANTs/pull/1879
  • ENH: Allow writing Jacobian matrix as NIFTI by @cookpa in https://github.com/ANTsX/ANTs/pull/1885
  • BUG: Jacobian determinants incorrect for non-identity direction matrices by @cookpa in https://github.com/ANTsX/ANTs/pull/1887

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.6.0...v2.6.1

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Published by cookpa 9 months ago

ants - Ktunaxia

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

New Contributors

  • @mathdugre made their first contribution in https://github.com/ANTsX/ANTs/pull/1838

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.5.4...v2.6.0

- C++
Published by cookpa 11 months ago

ants - Kotshkorkia

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

New Contributors

  • @NicolasGensollen made their first contribution in https://github.com/ANTsX/ANTs/pull/1781

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.5.3...v2.5.4

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Published by cookpa over 1 year ago

ants - Gracilidris

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

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.5.2...v2.5.3

- C++
Published by cookpa over 1 year ago

ants - Froggattella

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 https://github.com/InsightSoftwareConsortium/ITK/pull/4630.

What's Changed

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

New Contributors

  • @mabulnaga made their first contribution in https://github.com/ANTsX/ANTs/pull/1719

Full Changelog: https://github.com/ANTsX/ANTs/compare/v2.5.1...v2.5.2

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Published by cookpa almost 2 years ago

ants - Forelius

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.

What's Changed

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

New Contributors

  • @dzenanz made their first contribution in https://github.com/ANTsX/ANTs/pull/1650
  • @jennydaman made their first contribution in https://github.com/ANTsX/ANTs/pull/1647

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

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Published by cookpa about 2 years ago

ants - Eurymyrmex

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

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

- C++
Published by cookpa over 2 years ago

ants - Eotapinoma

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 https://github.com/ANTsX/ANTs/pull/1478
  • ENH: Use ITK ZLIB, test release builds, Windows binaries (#1) by @cookpa in https://github.com/ANTsX/ANTs/pull/1484
  • COMP: Update actions to resolve deprecation warnings by @cookpa in https://github.com/ANTsX/ANTs/pull/1485
  • COMP: Update docker login action by @cookpa in https://github.com/ANTsX/ANTs/pull/1486
  • SVN → Git by @DimitriPapadopoulos in https://github.com/ANTsX/ANTs/pull/1506
  • ENH: Read Windows pointers by @cookpa in https://github.com/ANTsX/ANTs/pull/1513
  • BUG: Was counting newline in windows pointer string test by @cookpa in https://github.com/ANTsX/ANTs/pull/1515
  • ENH: Parse windows pointers for write operations [skip ci] by @cookpa in https://github.com/ANTsX/ANTs/pull/1516
  • Do not prepend v to version by @DimitriPapadopoulos in https://github.com/ANTsX/ANTs/pull/1504
  • Clarify antsBrainExtraction.sh usage by @cookpa in https://github.com/ANTsX/ANTs/pull/1520
  • Enable MINC support by default by @gdevenyi in https://github.com/ANTsX/ANTs/pull/1526
  • ENH: Clarify usage, skip intensity image if it is "none" or "na" by @cookpa in https://github.com/ANTsX/ANTs/pull/1530
  • DOC: Recommend Mattes MI as the default metric by @cookpa in https://github.com/ANTsX/ANTs/pull/1531
  • BUG: Enable sparse sampling of metrics in SyN registration by @ntustison in https://github.com/ANTsX/ANTs/commit/14e7312928179387e74a941f4b48223ffb9f4052

New Contributors

  • @DimitriPapadopoulos made their first contribution in https://github.com/ANTsX/ANTs/pull/1506

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

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Published by cookpa almost 3 years ago

ants - Emplastus

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 https://github.com/ANTsX/ANTs/pull/1434
  • ENH: Check AverageImages input files can be read by @cookpa in https://github.com/ANTsX/ANTs/pull/1436
  • COMP: Pass optimization flags to ITK and ANTS-build by @cookpa in https://github.com/ANTsX/ANTs/pull/1445
  • ENH: Install scripts for non-release configurations by @cookpa in https://github.com/ANTsX/ANTs/pull/1449
  • ENH: antsAtroposN4.sh - exposed more subcommand parameters as arguments by @br-cpvc in https://github.com/ANTsX/ANTs/pull/1420
  • STYLE: Clarify usage of antsAtroposN4.sh and make defaults visible by @cookpa in https://github.com/ANTsX/ANTs/pull/1450
  • BUG: Atropos no longer segfaults when -i is missing, it reports an error msg instead by @br-cpvc in https://github.com/ANTsX/ANTs/pull/1454
  • PERF: Bump ITK to control multi-threading in MI registration. by @cookpa in https://github.com/ANTsX/ANTs/pull/1455
  • BUG: fixed Scripts/antsAtroposN4.sh not stopping when subcommands exit with exitcode>0 by @br-cpvc in https://github.com/ANTsX/ANTs/pull/1456
  • BUG: Needed to exit immediately if mask is missing by @cookpa in https://github.com/ANTsX/ANTs/pull/1458
  • BUG: Need the slash on ANTSPATH by @cookpa in https://github.com/ANTsX/ANTs/pull/1457
  • PERF: accelerating antsAtroposSegmentationImageFilter.hxx function GetPosteriorProbabilityImage using ITK ParallelizeImageRegion by @br-cpvc in https://github.com/ANTsX/ANTs/pull/1462
  • ENH: Make "-u" option also set a random seed for registration by @cookpa in https://github.com/ANTsX/ANTs/pull/1468
  • BUG: Set sampling percentage and strategy for SyN by @ntustison in https://github.com/ANTsX/ANTs/commit/14e7312928179387e74a941f4b48223ffb9f4052
  • ENH: Set ITK version to 5.3.0 by @cookpa in https://github.com/ANTsX/ANTs/pull/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: https://github.com/ANTsX/ANTs/compare/v2.4.2...v2.4.3

- C++
Published by cookpa about 3 years ago

ants - Eldermyrmex

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

  • @br-cpvc made their first contribution in https://github.com/ANTsX/ANTs/pull/1422

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

- C++
Published by cookpa over 3 years ago

ants - Elaphrodites

What's Changed

  • ENH: Skip CI on the post-release commit by @cookpa in https://github.com/ANTsX/ANTs/pull/1385
  • ENH: Attach binaries to releases by @cookpa in https://github.com/ANTsX/ANTs/pull/1387
  • ENH: Progress reporting for antsAI by @cookpa in https://github.com/ANTsX/ANTs/pull/1389
  • BUG: Parse Release numbers > 9 properly by @cookpa in https://github.com/ANTsX/ANTs/pull/1391
  • ENH: Use docker to build Centos binaries by @cookpa in https://github.com/ANTsX/ANTs/pull/1393
  • ENH: Allow fixed,moving masks in scripts by @cookpa in https://github.com/ANTsX/ANTs/pull/1406
  • WIP: Remove unused estimate learning rate at each iteration. by @ntustison in https://github.com/ANTsX/ANTs/pull/1411
  • ENH: Output extra info at the end of registration by @cookpa in https://github.com/ANTsX/ANTs/pull/1415
  • BUG: Fix check for existing versions, other checks by @cookpa in https://github.com/ANTsX/ANTs/pull/1416

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

- C++
Published by cookpa over 3 years ago

ants - Elaeomyrmex

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

  • ENH: Add option for SyN gradient step in scripts by @cookpa in https://github.com/ANTsX/ANTs/pull/1129
  • BUG: ImageMath ExtractComponentFrom3DTensor was writing a tensor inst… by @cookpa in https://github.com/ANTsX/ANTs/pull/1139
  • Sharpening options in template construction by @cookpa in https://github.com/ANTsX/ANTs/pull/1149
  • DOC: Include version information and citation in docker images by @cookpa in https://github.com/ANTsX/ANTs/pull/1151
  • ENH: Fix timezone for CircleCI Docker builds by @cookpa in https://github.com/ANTsX/ANTs/pull/1153
  • ENH: Set Docker container creation timezone by @cookpa in https://github.com/ANTsX/ANTs/pull/1154
  • ENH: Hopefully push tagged versions to DockerHub by @cookpa in https://github.com/ANTsX/ANTs/pull/1156
  • ENH: Add kinematics tensors. by @ntustison in https://github.com/ANTsX/ANTs/pull/1158
  • Antsct usage by @cookpa in https://github.com/ANTsX/ANTs/pull/1159
  • Update antsRegistration.cxx by @andife in https://github.com/ANTsX/ANTs/pull/1175
  • Update antsRegistrationSyNQuick.sh by @andife in https://github.com/ANTsX/ANTs/pull/1176
  • ENH: Repro. by @ntustison in https://github.com/ANTsX/ANTs/pull/1190
  • ENH: Accommodate AFNI stats images. by @ntustison in https://github.com/ANTsX/ANTs/pull/1191
  • ENH: Allow user to set random seed in repro mode by @cookpa in https://github.com/ANTsX/ANTs/pull/1196
  • BUG: Fix precision issues causing priors to get zeroed out by @cookpa in https://github.com/ANTsX/ANTs/pull/1197
  • Fix mismatch ambiguous size compilation error by @hjmjohnson in https://github.com/ANTsX/ANTs/pull/1209
  • BUG: Fix build of sccan with C++14 or later by @ghisvail in https://github.com/ANTsX/ANTs/pull/1214
  • COMP: Use modern ITK paradigms by @hjmjohnson in https://github.com/ANTsX/ANTs/pull/1218
  • ENH: Update issue templates, add PR template by @cookpa in https://github.com/ANTsX/ANTs/pull/1220
  • Template initialization to improve convergence by @cookpa in https://github.com/ANTsX/ANTs/pull/1227
  • DOC: Latest attempt to encourage use of issue templates [skip ci] by @cookpa in https://github.com/ANTsX/ANTs/pull/1230
  • Added support for IBM POWER8/9 architectures by @pantaray in https://github.com/ANTsX/ANTs/pull/1243
  • BUG - antsIntermodalityIntrasubject.sh - fixed a typo and incorrect running summary by @nirso in https://github.com/ANTsX/ANTs/pull/1247
  • COMP: use sha512 instead of md5 hashes for ExternalData fetching by @bcdarwin in https://github.com/ANTsX/ANTs/pull/1237
  • BUG: Add bc to Docker, needed for antsAtroposN4.sh by @cookpa in https://github.com/ANTsX/ANTs/pull/1254
  • ENH: Use GNUInstallDirs CMake module by @gdevenyi in https://github.com/ANTsX/ANTs/pull/1062
  • ENH: Version info in repo by @cookpa in https://github.com/ANTsX/ANTs/pull/1246
  • ENH: Allow users to specify an initial transform by @cookpa in https://github.com/ANTsX/ANTs/pull/1255
  • BUG: Output correct number of iterations in parameter summary by @cookpa in https://github.com/ANTsX/ANTs/pull/1257
  • COMP: comment out WriteImage as in the rest of the file by @simonoxen in https://github.com/ANTsX/ANTs/pull/1260
  • BUG: Lesions in background or surrounded by darker tissue could cause… by @cookpa in https://github.com/ANTsX/ANTs/pull/1265
  • Allow build with ITK 5.3 by @hjmjohnson in https://github.com/ANTsX/ANTs/pull/1279
  • Fix joint fusion bugs multi modal data by @hjmjohnson in https://github.com/ANTsX/ANTs/pull/1302
  • COMP: Fix compilation syntax errors from failed build by @hjmjohnson in https://github.com/ANTsX/ANTs/pull/1303
  • Minor formatting issues by @hjmjohnson in https://github.com/ANTsX/ANTs/pull/1304
  • COMP: Update ITK and VTK to avoid compiler warnings by @hjmjohnson in https://github.com/ANTsX/ANTs/pull/1305
  • ENH: Allow writing HDF5 transforms as ITK transforms by @cookpa in https://github.com/ANTsX/ANTs/pull/1317
  • ENH: Use https for git URLs by @cookpa in https://github.com/ANTsX/ANTs/pull/1324
  • ENH: Build docker images using Github Actions by @cookpa in https://github.com/ANTsX/ANTs/pull/1332
  • DOC: Docker CI badge in README by @cookpa in https://github.com/ANTsX/ANTs/pull/1333
  • BUG: Need to install bc in final layer by @cookpa in https://github.com/ANTsX/ANTs/pull/1334
  • ENH: Allow smoothing to be specified in mm or vox by @cookpa in https://github.com/ANTsX/ANTs/pull/1350
  • ENH: Expose UseGradientFilter variable for image metrics. by @ntustison in https://github.com/ANTsX/ANTs/pull/1349
  • ENH: Expose gradient filter option for metrics. by @ntustison in https://github.com/ANTsX/ANTs/pull/1351
  • COMP: Find additional test data by @cookpa in https://github.com/ANTsX/ANTs/pull/1357
  • DOC: Better explain options by @cookpa in https://github.com/ANTsX/ANTs/pull/1358
  • ENH: Run short tests during build by @cookpa in https://github.com/ANTsX/ANTs/pull/1365
  • BUG: Some verbose output not properly guarded by an if statement by @cookpa in https://github.com/ANTsX/ANTs/pull/1367
  • STYLE: Catch exceptions by const reference by @hjmjohnson in https://github.com/ANTsX/ANTs/pull/1361
  • Const exceptions by @cookpa in https://github.com/ANTsX/ANTs/pull/1368
  • ENH: Denoise all anatomical images, but outside of loop by @cookpa in https://github.com/ANTsX/ANTs/pull/1373
  • Update to newest ITK hash by @gdevenyi in https://github.com/ANTsX/ANTs/pull/1382
  • WIP: Changes for updating to current ITK. by @ntustison in https://github.com/ANTsX/ANTs/pull/1355

New Contributors

  • @andife made their first contribution in https://github.com/ANTsX/ANTs/pull/1175
  • @ghisvail made their first contribution in https://github.com/ANTsX/ANTs/pull/1214
  • @pantaray made their first contribution in https://github.com/ANTsX/ANTs/pull/1243
  • @nirso made their first contribution in https://github.com/ANTsX/ANTs/pull/1247
  • @bcdarwin made their first contribution in https://github.com/ANTsX/ANTs/pull/1237
  • @simonoxen made their first contribution in https://github.com/ANTsX/ANTs/pull/1260

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

- C++
Published by cookpa over 3 years ago

ants - Ecphorella

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 ANTSUSEGIT_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.

- C++
Published by cookpa about 5 years ago

ants - Dorymyrmex

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

- C++
Published by cookpa over 5 years ago

ants - Leptomyrmex

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

- C++
Published by stnava over 5 years ago

ants - Iridomyrmex

WIP: this is a first attempt at an updated release with new ITK etc.

Update 10/30/19: This release has a bug in antsRegistration that causes the iterations per level to be incorrect. An index offset shifts the number of iterations by one level, so if you specify -c AxBxCxD, the actual iterations performed will be BxCxDxE, where E is an undetermined unsigned integer. A fix is available here https://github.com/ANTsX/ANTs/commit/3d416475b296321dfe5e6cf905e05f197f4afb52.

- C++
Published by stnava over 6 years ago

ants - Black Garden II

  • improves on v5 compatibility

- C++
Published by stnava over 7 years ago

ants - black garden

  • uses recent ITKv5 performance enhancements

  • one may enforce reproducibility be setting the random seed and using a single execution thread.

  • improvements to antsAI

  • random bug fixes in scripts/code ( see commits )

  • style enhancements

  • generalization of types

  • ants longitudinal image processing pipeline

  • longitudinal JLF

  • MeasureImageSimilarity refactoring

- C++
Published by stnava over 7 years ago

ants - matabele

First new release after two years. Will be updated with binaries as they become available.

  • Joint intensity fusion and new joint label fusion

  • longitudinal pipeline

  • asl tools

  • many bug fixes / documentation improvements

  • super-resolution

  • denoiser

  • antsSurf and antsVol

  • MINC transformations

  • jacobian fixes / tests

  • eigenanatomy and sccan improvements

  • style improvements

  • several travis-related updates

  • area fixes / estimates

the etymology of the release name here

- C++
Published by stnava almost 9 years ago

ants - ANTs Version 2.1.0

- C++
Published by armaneshaghi about 11 years ago