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 #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

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 #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

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 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

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.

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

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 #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

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 #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

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 #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

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

• @br-cpvc made their first contribution in #1422

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

Elaphrodites

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

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

New Contributors

• @andife made their first contribution in #1175
• @ghisvail made their first contribution in #1214
• @pantaray made their first contribution in #1243
• @nirso made their first contribution in #1247
• @bcdarwin made their first contribution in #1237
• @simonoxen made their first contribution in #1260

Full Changelog: v2.3.5...v2.4.0