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

0.7.0

What's Changed

🛠 Breaking Changes

• Rename QC metrics and output QC files as TSVs by @tsalo in #375
• Move atlases into a subfolder by @tsalo in #377

🎉 Exciting New Features

• Add --ignore fmap-jacobian option by @tsalo in #385
• Support lists in filter file with * or null by @tsalo in #388

🐛 Bug Fixes

• Flip order of transforms in init_ds_volumes_wf by @tsalo in #392

Other Changes

• Use space definitions from niworkflows by @tsalo in #378
• Use niworkflows enhance-and-skullstrip workflow by @tsalo in #371
• Update Nilearn requirement to 0.10.3 by @tsalo in #396
• [ENH] Update docker image by @mattcieslak in #409
• [FIX] update to newer docker by @mattcieslak in #412
• Update codecov orb version by @tsalo in #410

Full Changelog: 0.6.0...0.7.0

0.6.0

This release makes substantial changes to ASLPrep.
The two main changes are (1) the Schaefer atlases are replaced with the PennLINC team's new 4S atlases, which combine the Schaefer cortical atlases and several subcortical atlases, and (2) a major rearchitect of the package based on fMRIPrep version 23.2.0a2. The latter allows ASLPrep to write out CIFTI and GIFTI format derivatives, and fixes SDC support (although SDC support is dependent on the next SDCFlows release, so in practice it won't work just yet).

I'd like to credit Chris Markiewicz (@effigies) for doing the majority of the work in the fMRIPrep refactor.

What's Changed

🛠 Breaking Changes

• Add AtlasPack atlases by @tsalo in #330
• Replace AtlasPack 0.0.5 atlases with AtlasPack 0.1.0 atlases by @tsalo in #334
• Remove sdcflows and model ASLPrep on fMRIPrep/next by @tsalo in #338

🎉 Exciting New Features

• Write out GIFTI and CIFTI CBF maps by @tsalo in #361

🐛 Bug Fixes

• Pin scipy version to 1.10.1 by @tsalo in #333
• Raise error if no M0 volume(s)/estimate available and background suppression is enabled by @tsalo in #337
• Limit BASIL --slicedt argument to ascending slice orders by @tsalo in #348
• Fix several warnings by @tsalo in #364

Other Changes

• Add 0.5.x release notes to changelog by @tsalo in #339
• Add dependabot Action by @tsalo in #365
• Fix fMRIPrep-related bugs by @tsalo in #366
• Prepare for 0.6.0 release by @tsalo in #362

New Contributors

• @dependabot made their first contribution in #367

Full Changelog: 0.5.1...0.6.0

0.6.0rc1

What's Changed

🛠 Breaking Changes

• Add AtlasPack atlases by @tsalo in #330

🐛 Bug Fixes

• Pin scipy version to 1.10.1 by @tsalo in #333

Full Changelog: 0.5.1...0.6.0rc1

0.5.1

What's Changed

🐛 Bug Fixes

• Make M0 TR optional for BASIL by @tsalo in #323
• Fix BolusCutOffTechnique typo by @tsalo in #328

Other Changes

• Remove unnecessary dependencies by @tsalo in #325
• Document M0 use in reports by @tsalo in #329

Full Changelog: 0.5.0...0.5.1

0.5.1rc1

What's Changed

🐛 Bug Fixes

• Make M0 TR optional for BASIL by @tsalo in #323

Full Changelog: 0.5.0...0.5.1rc1

0.5.0

What's Changed

🎉 Exciting New Features

• Add force-ge and force-no-ge parameters by @tsalo in #313
• Write out QC metadata by @tsalo in #317

🐛 Bug Fixes

• Fix nibabel import by @tsalo in #301
• Fix the Docker image by @tsalo in #312
• Remove M0 metadata from multi-PLD GE metadata dictionary by @tsalo in #315
• Fix CombineMotionParameters to support single-volume volume types by @tsalo in #316
• Patch regmotoasl by @tsalo in #320
• Patch regmotoasl again by @tsalo in #321

Other Changes

• Replace niworkflows calls with dependency calls (second attempt) by @tsalo in #299
• Adopt Nipreps configuration and maintenance docs by @tsalo in #231
• Fix Docker build steps by @tsalo in #309

Full Changelog: 0.4.0...0.5.0

0.4.0

This release re-implements multi-delay PCASL and single-delay Q2TIPS PASL support.

Additionally, we have replaced certain BOLD-specific steps with ASL-compatible alternatives. One such case is slice timing correction. Rather than interpolate the ASL time series to perform slice timing correction (as in BOLD preprocessing), ASLPrep now shifts PLDs according to the slice timing. The other major change is to motion correction, which is now performed separately for each image type in the ASL time series (e.g., control, label, and M0 volumes).

Thanks to Sudipto Dolui, Jian Hu, Jan Petr, Manuel Taso, and Kay Jann for their help and feedback.

What's Changed

🛠 Breaking Changes

• Use same TPM threshold for GE and non-GE data by @tsalo in #263
• Remove slice-timing correction by @tsalo in #269

🎉 Exciting New Features

• Shift PostLabelingDelay(s) by slice times by @tsalo in #280
• Perform motion correction separately for each image type by @tsalo in #275
• Support single-PLD Q2TIPS PASL and multi-PLD PCASL by @tsalo in #268

🐛 Bug Fixes

• Support runs with SCORE/SCRUB disabled by @tsalo in #279
• Reorganize atlases and add them to the package data by @tsalo in #282

Other Changes

• Refactor workflow connections by @tsalo in #261
• Refactor more by @tsalo in #264
• Remove unused workflows by @tsalo in #271
• Remove test-made nifti files before storing artifacts by @tsalo in #274
• Improve plots by @tsalo in #286
• Remove multi-echo elements by @tsalo in #294
• Document M0 scaling by @tsalo in #292

Full Changelog: 0.3.0...0.4.0