25.1.0

This release brings ASLPrep in line with sMRIPrep version 0.19.1, which produces a number of additional outputs, including a cortex mask and the goodvoxels mask.

What's Changed

🐛 Bug Fixes

• Replace instances of fmriprep_dir with aslprep_dir by @tsalo in #589

Other Changes

• Update smriprep requirement from ~=0.18.0 to ~=0.19.1 and reproduce fMRIPrep PRs by @dependabot[bot] in #588

Full Changelog: 25.0.0...25.1.0

25.0.0

What's Changed

🛠 Breaking Changes

• Implement general kinetic model for multi-PLD data by @tsalo in #545

🎉 Exciting New Features

• Scale M0 scans with short TRs according to Alsop 2015 by @tsalo in #532
• Use Gaussian interpolation for resampling tissue probability maps by @tsalo in #542
• Incorporate sliceband in oxford_asl call for multiband ASL by @tsalo in #548
• Add figure plotting brain mask by @tsalo in #547
• Add disable-n4 option by @tsalo in #583

🐛 Bug Fixes

• Add legend to figures by @tsalo in #482
• fix: Find aslrefs in precomputed derivatives, remove bad connection by @effigies in #518
• Add boilerplate elements to templates by @tsalo in #524
• FIX: Change MCFLIRT cost function to Mutual Information by @aptinis in #525
• Write out aslref CBF + ATT in minimal mode by @tsalo in #522
• Use node's working directory as output directory for BASIL by @tsalo in #552
• Allow duplicate keys in get_sbrefs by @tsalo in #555
• Apply MCFLIRT to register m0scan to aslref image by @tsalo in #553
• Resample M0 scan to ASL resolution by @tsalo in #556
• Fix tau array generation for multi-delay data by @tsalo in #568
• Fix resolution entity by @tsalo in #584

Other Changes

• Fix spelling errors in code by @tsalo in #488
• Bring ASLPrep in line with fMRIPrep 25.0.0 by @tsalo in #510
• Remove dummy scan-related code by @tsalo in #526
• chore: Replace niworkflows reporting tools with nireports by @effigies in #527
• Calculate the components of QEI independently for group reports by @mattcieslak in #523
• rf: Split fieldmap registration into its own fit step by @effigies in #531
• Speed up integration tests by @tsalo in #535
• Clarify cli help messages by @tien-tong in #533
• Speed up FreeSurfer BBR in the CI tests by @mattcieslak in #543
• Replace BOLD and EPI with ASL in code by @tsalo in #537
• Fix typos in documentation and add page on BIDS curation by @B-Sevchik in #529
• Fix typos in report specifications by @tsalo in #554
• Add new contributors and available ORCIDs to CITATION.cff by @tsalo in #559
• Bump transforms3d version by @tsalo in #581

New Contributors

• @effigies made their first contribution in #518
• @aptinis made their first contribution in #525
• @tien-tong made their first contribution in #533
• @B-Sevchik made their first contribution in #529

Full Changelog: 0.7.5...25.0.0

25.0.0rc1

Highlights

• We are switching from semantic versioning (MAJOR.MINOR.PATCH) to calendar versioning (YEAR.MINOR.PATCH) to match the versioning of fMRIPrep.
• This release brings ASLPrep up to date with fMRIPrep version 25.0.0.
• We have replaced the weighted average method for multi-delay data with a two-compartment general kinetic model, which (1) should improve CBF and ATT estimation, (2) allows ASLPrep to process multi-delay PASL data, and (3) generates aBAT and aBV outputs.
• We changed the cost function for motion correction, which dramatically improves motion correction on multi-delay data when the contrast varies over delays.

What's Changed

🛠 Breaking Changes

• Implement general kinetic model for multi-PLD data by @tsalo in #545

🎉 Exciting New Features

• Scale M0 scans with short TRs according to Alsop 2015 by @tsalo in #532
• Use Gaussian interpolation for resampling tissue probability maps by @tsalo in #542
• Incorporate sliceband in oxford_asl call for multiband ASL by @tsalo in #548
• Add figure plotting brain mask by @tsalo in #547

🐛 Bug Fixes

• Add legend to figures by @tsalo in #482
• fix: Find aslrefs in precomputed derivatives, remove bad connection by @effigies in #518
• Add boilerplate elements to templates by @tsalo in #524
• FIX: Change MCFLIRT cost function to Mutual Information by @aptinis in #525
• Write out aslref CBF + ATT in minimal mode by @tsalo in #522
• Use node's working directory as output directory for BASIL by @tsalo in #552
• Allow duplicate keys in get_sbrefs by @tsalo in #555
• Apply MCFLIRT to register m0scan to aslref image by @tsalo in #553
• Resample M0 scan to ASL resolution by @tsalo in #556

Other Changes

• Fix spelling errors in code by @tsalo in #488
• Bring ASLPrep in line with fMRIPrep 25.0.0 by @tsalo in #510
• Remove dummy scan-related code by @tsalo in #526
• chore: Replace niworkflows reporting tools with nireports by @effigies in #527
• Calculate the components of QEI independently for group reports by @mattcieslak in #523
• rf: Split fieldmap registration into its own fit step by @effigies in #531
• Speed up integration tests by @tsalo in #535
• Clarify cli help messages by @tientong98 in #533
• Speed up FreeSurfer BBR in the CI tests by @mattcieslak in #543
• Replace BOLD and EPI with ASL in code by @tsalo in #537
• Fix typos in documentation and add page on BIDS curation by @B-Sevchik in #529
• Fix typos in report specifications by @tsalo in #554
• Add new contributors and available ORCIDs to CITATION.cff by @tsalo in #559

New Contributors

• @effigies made their first contribution in #518
• @aptinis made their first contribution in #525
• @tientong98 made their first contribution in #533
• @B-Sevchik made their first contribution in #529

Full Changelog: 0.7.5...25.0.0rc1

0.7.5

What's Changed

🛠 Breaking Changes

• Fix volume selection and temporarily remove --dummy-scans parameter by @tsalo in #468

🎉 Exciting New Features

• Output fsLR meshes on subject surfaces by @tsalo in #478

🐛 Bug Fixes

• Fix CBF CIFTI generation when --project-goodvoxels is enabled by @tsalo in #460
• Return the mean M0 TR in ExtractCBF by @tsalo in #470

Other Changes

• Upgrade to deno-based BIDS validator by @tsalo in #467

Full Changelog: 0.7.4...0.7.5

0.7.5rc2

What's Changed

🛠 Breaking Changes

• Fix volume selection and temporarily remove --dummy-scans parameter by @tsalo in #468

🐛 Bug Fixes

• Return the mean M0 TR in ExtractCBF by @tsalo in #470

Other Changes

• Upgrade to deno-based BIDS validator by @tsalo in #467

Full Changelog: 0.7.5rc1...0.7.5rc2

0.7.5rc1

What's Changed

🐛 Bug Fixes

• Fix CBF CIFTI generation when --project-goodvoxels is enabled by @tsalo in #460

Full Changelog: 0.7.4...0.7.5rc1

0.7.4

What's Changed

🛠 Breaking Changes

• Bring up to date with fMRIPrep 24.1.1 by @tsalo in #455

Full Changelog: 0.7.3...0.7.4

0.7.3

This release fixes a bug in multi-PLD PCASL CBF calculation. Thanks to @xu-boyan for identifying the problem!

What's Changed

🐛 Bug Fixes

• Add t1tissue term to multi-delay CBF formula by @tsalo in #432

Full Changelog: 0.7.2...0.7.3

0.7.2

A patch release to fix GIFTI outputs.

What's Changed

🐛 Bug Fixes

• Split giftis by hemisphere by @tsalo in #419

Full Changelog: 0.7.1...0.7.2

0.7.1

A hotfix release following 0.7.0.

What's Changed

🐛 Bug Fixes

• Fix the entrypoint path in the Dockerfile by @tsalo in #413

Full Changelog: 0.7.0...0.7.1