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