Skip to content

Releases: ANTsX/ANTs

Gracilidris

24 Jul 14:57
Compare
Choose a tag to compare

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

What's Changed

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

Froggattella

16 May 15:20
Compare
Choose a tag to compare

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

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

Forelius

24 Jan 19:57
Compare
Choose a tag to compare

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

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

Eurymyrmex

28 Aug 15:00
Compare
Choose a tag to compare

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: v2.4.4...v2.5.0

Eotapinoma

01 May 15:39
Compare
Choose a tag to compare

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: v2.4.3...v2.4.4

Emplastus

06 Jan 16:17
Compare
Choose a tag to compare

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

Eldermyrmex

18 Oct 00:12
Compare
Choose a tag to compare

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 #1422
  • DOC: added missing end parenthesis to Atropos documentation string by @br-cpvc in #1421

New Contributors

Full Changelog: v2.4.1...v2.4.2

Elaphrodites

23 Aug 20:08
Compare
Choose a tag to compare

What's Changed

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

Full Changelog: v2.4.0...v2.4.1

Elaeomyrmex

06 Jul 14:40
Compare
Choose a tag to compare

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: v2.3.5...v2.4.0

Ecphorella

21 Dec 15:05
6f13702
Compare
Choose a tag to compare

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.