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Recent Releases of aslprep

aslprep - 25.0.0

What's Changed

🛠 Breaking Changes

  • Implement general kinetic model for multi-PLD data by @tsalo in https://github.com/PennLINC/aslprep/pull/545

🎉 Exciting New Features

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

🐛 Bug Fixes

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

Other Changes

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

New Contributors

  • @effigies made their first contribution in https://github.com/PennLINC/aslprep/pull/518
  • @aptinis made their first contribution in https://github.com/PennLINC/aslprep/pull/525
  • @tien-tong made their first contribution in https://github.com/PennLINC/aslprep/pull/533
  • @B-Sevchik made their first contribution in https://github.com/PennLINC/aslprep/pull/529

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.5...25.0.0

- Python
Published by tsalo 6 months ago

aslprep - 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 https://github.com/PennLINC/aslprep/pull/545 ### 🎉 Exciting New Features
  • Scale M0 scans with short TRs according to Alsop 2015 by @tsalo in https://github.com/PennLINC/aslprep/pull/532
  • Use Gaussian interpolation for resampling tissue probability maps by @tsalo in https://github.com/PennLINC/aslprep/pull/542
  • Incorporate sliceband in oxford_asl call for multiband ASL by @tsalo in https://github.com/PennLINC/aslprep/pull/548
  • Add figure plotting brain mask by @tsalo in https://github.com/PennLINC/aslprep/pull/547 ### 🐛 Bug Fixes
  • Add legend to figures by @tsalo in https://github.com/PennLINC/aslprep/pull/482
  • fix: Find aslrefs in precomputed derivatives, remove bad connection by @effigies in https://github.com/PennLINC/aslprep/pull/518
  • Add boilerplate elements to templates by @tsalo in https://github.com/PennLINC/aslprep/pull/524
  • FIX: Change MCFLIRT cost function to Mutual Information by @aptinis in https://github.com/PennLINC/aslprep/pull/525
  • Write out aslref CBF + ATT in minimal mode by @tsalo in https://github.com/PennLINC/aslprep/pull/522
  • Use node's working directory as output directory for BASIL by @tsalo in https://github.com/PennLINC/aslprep/pull/552
  • Allow duplicate keys in get_sbrefs by @tsalo in https://github.com/PennLINC/aslprep/pull/555
  • Apply MCFLIRT to register m0scan to aslref image by @tsalo in https://github.com/PennLINC/aslprep/pull/553
  • Resample M0 scan to ASL resolution by @tsalo in https://github.com/PennLINC/aslprep/pull/556 ### Other Changes
  • Fix spelling errors in code by @tsalo in https://github.com/PennLINC/aslprep/pull/488
  • Bring ASLPrep in line with fMRIPrep 25.0.0 by @tsalo in https://github.com/PennLINC/aslprep/pull/510
  • Remove dummy scan-related code by @tsalo in https://github.com/PennLINC/aslprep/pull/526
  • chore: Replace niworkflows reporting tools with nireports by @effigies in https://github.com/PennLINC/aslprep/pull/527
  • Calculate the components of QEI independently for group reports by @mattcieslak in https://github.com/PennLINC/aslprep/pull/523
  • rf: Split fieldmap registration into its own fit step by @effigies in https://github.com/PennLINC/aslprep/pull/531
  • Speed up integration tests by @tsalo in https://github.com/PennLINC/aslprep/pull/535
  • Clarify cli help messages by @tientong98 in https://github.com/PennLINC/aslprep/pull/533
  • Speed up FreeSurfer BBR in the CI tests by @mattcieslak in https://github.com/PennLINC/aslprep/pull/543
  • Replace BOLD and EPI with ASL in code by @tsalo in https://github.com/PennLINC/aslprep/pull/537
  • Fix typos in documentation and add page on BIDS curation by @B-Sevchik in https://github.com/PennLINC/aslprep/pull/529
  • Fix typos in report specifications by @tsalo in https://github.com/PennLINC/aslprep/pull/554
  • Add new contributors and available ORCIDs to CITATION.cff by @tsalo in https://github.com/PennLINC/aslprep/pull/559

New Contributors

  • @effigies made their first contribution in https://github.com/PennLINC/aslprep/pull/518
  • @aptinis made their first contribution in https://github.com/PennLINC/aslprep/pull/525
  • @tientong98 made their first contribution in https://github.com/PennLINC/aslprep/pull/533
  • @B-Sevchik made their first contribution in https://github.com/PennLINC/aslprep/pull/529

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.5...25.0.0rc1

- Python
Published by tsalo 9 months ago

aslprep - 0.7.5

What's Changed

🛠 Breaking Changes

  • Fix volume selection and temporarily remove --dummy-scans parameter by @tsalo in https://github.com/PennLINC/aslprep/pull/468 ### 🎉 Exciting New Features
  • Output fsLR meshes on subject surfaces by @tsalo in https://github.com/PennLINC/aslprep/pull/478 ### 🐛 Bug Fixes
  • Fix CBF CIFTI generation when --project-goodvoxels is enabled by @tsalo in https://github.com/PennLINC/aslprep/pull/460
  • Return the mean M0 TR in ExtractCBF by @tsalo in https://github.com/PennLINC/aslprep/pull/470 ### Other Changes
  • Upgrade to deno-based BIDS validator by @tsalo in https://github.com/PennLINC/aslprep/pull/467

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.4...0.7.5

- Python
Published by tsalo about 1 year ago

aslprep - 0.7.5rc2

What's Changed

🛠 Breaking Changes

  • Fix volume selection and temporarily remove --dummy-scans parameter by @tsalo in https://github.com/PennLINC/aslprep/pull/468

🐛 Bug Fixes

  • Return the mean M0 TR in ExtractCBF by @tsalo in https://github.com/PennLINC/aslprep/pull/470

Other Changes

  • Upgrade to deno-based BIDS validator by @tsalo in https://github.com/PennLINC/aslprep/pull/467

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.5rc1...0.7.5rc2

- Python
Published by tsalo about 1 year ago

aslprep - 0.7.5rc1

What's Changed

🐛 Bug Fixes

  • Fix CBF CIFTI generation when --project-goodvoxels is enabled by @tsalo in https://github.com/PennLINC/aslprep/pull/460

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.4...0.7.5rc1

- Python
Published by tsalo over 1 year ago

aslprep - 0.7.4

What's Changed

🛠 Breaking Changes

  • Bring up to date with fMRIPrep 24.1.1 by @tsalo in https://github.com/PennLINC/aslprep/pull/455

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.3...0.7.4

- Python
Published by tsalo over 1 year ago

aslprep - 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 https://github.com/PennLINC/aslprep/pull/432

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.2...0.7.3

- Python
Published by tsalo over 1 year ago

aslprep - 0.7.2

A patch release to fix GIFTI outputs. <!-- Release notes generated using configuration in .github/release.yml at main -->

What's Changed

🐛 Bug Fixes

  • Split giftis by hemisphere by @tsalo in https://github.com/PennLINC/aslprep/pull/419

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.1...0.7.2

- Python
Published by tsalo over 1 year ago

aslprep - 0.7.1

A hotfix release following 0.7.0. <!-- Release notes generated using configuration in .github/release.yml at main -->

What's Changed

🐛 Bug Fixes

  • Fix the entrypoint path in the Dockerfile by @tsalo in https://github.com/PennLINC/aslprep/pull/413

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.7.0...0.7.1

- Python
Published by tsalo almost 2 years ago

aslprep - 0.7.0

What's Changed

🛠 Breaking Changes

  • Rename QC metrics and output QC files as TSVs by @tsalo in https://github.com/PennLINC/aslprep/pull/375
  • Move atlases into a subfolder by @tsalo in https://github.com/PennLINC/aslprep/pull/377 ### 🎉 Exciting New Features
  • Add --ignore fmap-jacobian option by @tsalo in https://github.com/PennLINC/aslprep/pull/385
  • Support lists in filter file with * or null by @tsalo in https://github.com/PennLINC/aslprep/pull/388 ### 🐛 Bug Fixes
  • Flip order of transforms in init_ds_volumes_wf by @tsalo in https://github.com/PennLINC/aslprep/pull/392 ### Other Changes
  • Use space definitions from niworkflows by @tsalo in https://github.com/PennLINC/aslprep/pull/378
  • Use niworkflows enhance-and-skullstrip workflow by @tsalo in https://github.com/PennLINC/aslprep/pull/371
  • Update Nilearn requirement to 0.10.3 by @tsalo in https://github.com/PennLINC/aslprep/pull/396
  • [ENH] Update docker image by @mattcieslak in https://github.com/PennLINC/aslprep/pull/409
  • [FIX] update to newer docker by @mattcieslak in https://github.com/PennLINC/aslprep/pull/412
  • Update codecov orb version by @tsalo in https://github.com/PennLINC/aslprep/pull/410

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.6.0...0.7.0

- Python
Published by tsalo almost 2 years ago

aslprep - 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 https://github.com/PennLINC/aslprep/pull/330
  • Replace AtlasPack 0.0.5 atlases with AtlasPack 0.1.0 atlases by @tsalo in https://github.com/PennLINC/aslprep/pull/334
  • Remove sdcflows and model ASLPrep on fMRIPrep/next by @tsalo in https://github.com/PennLINC/aslprep/pull/338 ### 🎉 Exciting New Features
  • Write out GIFTI and CIFTI CBF maps by @tsalo in https://github.com/PennLINC/aslprep/pull/361 ### 🐛 Bug Fixes
  • Pin scipy version to 1.10.1 by @tsalo in https://github.com/PennLINC/aslprep/pull/333
  • Raise error if no M0 volume(s)/estimate available and background suppression is enabled by @tsalo in https://github.com/PennLINC/aslprep/pull/337
  • Limit BASIL --slicedt argument to ascending slice orders by @tsalo in https://github.com/PennLINC/aslprep/pull/348
  • Fix several warnings by @tsalo in https://github.com/PennLINC/aslprep/pull/364 ### Other Changes
  • Add 0.5.x release notes to changelog by @tsalo in https://github.com/PennLINC/aslprep/pull/339
  • Add dependabot Action by @tsalo in https://github.com/PennLINC/aslprep/pull/365
  • Fix fMRIPrep-related bugs by @tsalo in https://github.com/PennLINC/aslprep/pull/366
  • Prepare for 0.6.0 release by @tsalo in https://github.com/PennLINC/aslprep/pull/362

New Contributors

  • @dependabot made their first contribution in https://github.com/PennLINC/aslprep/pull/367

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.5.1...0.6.0

- Python
Published by tsalo about 2 years ago

aslprep - 0.6.0rc1

What's Changed

🛠 Breaking Changes

  • Add AtlasPack atlases by @tsalo in https://github.com/PennLINC/aslprep/pull/330 ### 🐛 Bug Fixes
  • Pin scipy version to 1.10.1 by @tsalo in https://github.com/PennLINC/aslprep/pull/333

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.5.1...0.6.0rc1

- Python
Published by tsalo over 2 years ago

aslprep - 0.5.1

What's Changed

🐛 Bug Fixes

  • Make M0 TR optional for BASIL by @tsalo in https://github.com/PennLINC/aslprep/pull/323
  • Fix BolusCutOffTechnique typo by @tsalo in https://github.com/PennLINC/aslprep/pull/328 ### Other Changes
  • Remove unnecessary dependencies by @tsalo in https://github.com/PennLINC/aslprep/pull/325
  • Document M0 use in reports by @tsalo in https://github.com/PennLINC/aslprep/pull/329

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.5.0...0.5.1

- Python
Published by tsalo over 2 years ago

aslprep - 0.5.1rc1

What's Changed

🐛 Bug Fixes

  • Make M0 TR optional for BASIL by @tsalo in https://github.com/PennLINC/aslprep/pull/323

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.5.0...0.5.1rc1

- Python
Published by tsalo over 2 years ago

aslprep - 0.5.0

What's Changed

🎉 Exciting New Features

  • Add force-ge and force-no-ge parameters by @tsalo in https://github.com/PennLINC/aslprep/pull/313
  • Write out QC metadata by @tsalo in https://github.com/PennLINC/aslprep/pull/317 ### 🐛 Bug Fixes
  • Fix nibabel import by @tsalo in https://github.com/PennLINC/aslprep/pull/301
  • Fix the Docker image by @tsalo in https://github.com/PennLINC/aslprep/pull/312
  • Remove M0 metadata from multi-PLD GE metadata dictionary by @tsalo in https://github.com/PennLINC/aslprep/pull/315
  • Fix CombineMotionParameters to support single-volume volume types by @tsalo in https://github.com/PennLINC/aslprep/pull/316
  • Patch regmotoasl by @tsalo in https://github.com/PennLINC/aslprep/pull/320
  • Patch regmotoasl again by @tsalo in https://github.com/PennLINC/aslprep/pull/321 ### Other Changes
  • Replace niworkflows calls with dependency calls (second attempt) by @tsalo in https://github.com/PennLINC/aslprep/pull/299
  • Adopt Nipreps configuration and maintenance docs by @tsalo in https://github.com/PennLINC/aslprep/pull/231
  • Fix Docker build steps by @tsalo in https://github.com/PennLINC/aslprep/pull/309

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.4.0...0.5.0

- Python
Published by tsalo over 2 years ago

aslprep - 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 https://github.com/PennLINC/aslprep/pull/263
  • Remove slice-timing correction by @tsalo in https://github.com/PennLINC/aslprep/pull/269 ### 🎉 Exciting New Features
  • Shift PostLabelingDelay(s) by slice times by @tsalo in https://github.com/PennLINC/aslprep/pull/280
  • Perform motion correction separately for each image type by @tsalo in https://github.com/PennLINC/aslprep/pull/275
  • Support single-PLD Q2TIPS PASL and multi-PLD PCASL by @tsalo in https://github.com/PennLINC/aslprep/pull/268 ### 🐛 Bug Fixes
  • Support runs with SCORE/SCRUB disabled by @tsalo in https://github.com/PennLINC/aslprep/pull/279
  • Reorganize atlases and add them to the package data by @tsalo in https://github.com/PennLINC/aslprep/pull/282 ### Other Changes
  • Refactor workflow connections by @tsalo in https://github.com/PennLINC/aslprep/pull/261
  • Refactor more by @tsalo in https://github.com/PennLINC/aslprep/pull/264
  • Remove unused workflows by @tsalo in https://github.com/PennLINC/aslprep/pull/271
  • Remove test-made nifti files before storing artifacts by @tsalo in https://github.com/PennLINC/aslprep/pull/274
  • Improve plots by @tsalo in https://github.com/PennLINC/aslprep/pull/286
  • Remove multi-echo elements by @tsalo in https://github.com/PennLINC/aslprep/pull/294
  • Document M0 scaling by @tsalo in https://github.com/PennLINC/aslprep/pull/292

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.3.0...0.4.0

- Python
Published by tsalo over 2 years ago

aslprep - 0.3.0

0.3.0 reflects renewed maintenance for ASLPrep.

The primary focuses of this release are: (1) fixing easily-fixable bugs, (2) disabling broken features with difficult-to-fix bugs, (3) cleaning up the codebase, (4) expanding test coverage, and (5) ensuring that outputs are BIDS-compliant.

To that end, we have unfortunately had to temporarily drop support for multi-PostLabelingDelay data, as well as PASL data with the Q2TIPS BolusCutOffTechnique. We will work on fixing these features for the next release.

Additionally, this release includes a number of breaking changes. We have renamed several of the outputs to ensure that they are BIDS-compliant. These outputs may need to change again in the future, but that will happen in the next minor release (0.4.0) at the earliest. See the table below for a list of the changed filenames.

| Description | <0.3.0 | 0.3.0 | |---|---|---| | CBF time series | _cbf.nii.gz | _desc-timeseries_cbf.nii.gz | | Mean CBF | _mean_cbf.nii.gz | _cbf.nii.gz | | CBF time series after SCORE denoising | _desc-score_cbf.nii.gz | _desc-scoreTimeseries_cbf.nii.gz | | Mean CBF after SCORE denoising | _desc-score_mean_cbf.nii.gz | _desc-score_cbf.nii.gz | | Bolus arrival time/arterial transit time | _desc-bat_cbf.nii.gz | _att.nii.gz |

Additionally, we have changed the atlases that are used for the parcellated CBF files. We have brought the atlases in line with those used by XCP-D. However, in the near future, we plan to update these atlases again, so that they are synchronized across ASLPrep, XCP-D, and QSIPrep, so please be aware of that upcoming change. <!-- Release notes generated using configuration in .github/release.yml at main -->

What's Changed

🛠 Breaking Changes

  • Rename BIDS-noncompliant derivatives by @tsalo in https://github.com/PennLINC/aslprep/pull/216
  • Use correct bolus values in CBF calculation and temporarily disable Q2TIPS, multi-PLD, and no-BolusCutOff processing by @tsalo in https://github.com/PennLINC/aslprep/pull/235
  • Disable SCORE/SCRUB for GE/short runs and get GE workflow working by @tsalo in https://github.com/PennLINC/aslprep/pull/248
  • Parallelize parcellation and replace atlases by @tsalo in https://github.com/PennLINC/aslprep/pull/254
  • Remove "mean" from mean CBF filenames and add "timeseries" to 4D CBF filenames by @tsalo in https://github.com/PennLINC/aslprep/pull/257 ### 🎉 Exciting New Features
  • Hardcode T1blood for some field strengths and use Zhang 2013 formula for others by @tsalo in https://github.com/PennLINC/aslprep/pull/243
  • Estimate labeling efficiency based on ASL type and number of background suppression pulses by @tsalo in https://github.com/PennLINC/aslprep/pull/244 ### 🐛 Bug Fixes
  • Pin looseversion by @tsalo in https://github.com/PennLINC/aslprep/pull/211
  • Correct ordering of probseg maps by @josephmje in https://github.com/PennLINC/aslprep/pull/192
  • Convert inversion times to a list for compatility with BASIL interface by @tsalo in https://github.com/PennLINC/aslprep/pull/222
  • Pin networkx version by @tsalo in https://github.com/PennLINC/aslprep/pull/227
  • Use LabelingEfficiency as BASIL --alpha parameter by @tsalo in https://github.com/PennLINC/aslprep/pull/233
  • Remove BIDS-noncompliant m0z and cbf files by @tsalo in https://github.com/PennLINC/aslprep/pull/236
  • Replace RepetitionTime with RepetitionTimePreparation by @tsalo in https://github.com/PennLINC/aslprep/pull/245
  • Index aslcontext rows with "cbf", not "CBF" by @tsalo in https://github.com/PennLINC/aslprep/pull/252 ### Other Changes
  • Use aslprep_build as base Docker image - attempt 2 by @tsalo in https://github.com/PennLINC/aslprep/pull/204
  • Autoformat with black and isort by @tsalo in https://github.com/PennLINC/aslprep/pull/205
  • Replace relative imports with absolute ones by @tsalo in https://github.com/PennLINC/aslprep/pull/206
  • Remove unused functions and classes by @tsalo in https://github.com/PennLINC/aslprep/pull/207
  • Rename PEP8-noncompliant classes by @tsalo in https://github.com/PennLINC/aslprep/pull/208
  • Consistently use f-strings for string formatting by @tsalo in https://github.com/PennLINC/aslprep/pull/209
  • Work on fixing docstrings and splitting modules by @tsalo in https://github.com/PennLINC/aslprep/pull/210
  • Remove unused arguments throughout package by @tsalo in https://github.com/PennLINC/aslprep/pull/212
  • Replace smriprep calls with dependency calls by @tsalo in https://github.com/PennLINC/aslprep/pull/217
  • Replace pybids calls with dependency calls by @tsalo in https://github.com/PennLINC/aslprep/pull/213
  • Use custom formatting for workflow connections by @tsalo in https://github.com/PennLINC/aslprep/pull/220
  • Improve documentation by @tsalo in https://github.com/PennLINC/aslprep/pull/218
  • Add step to run unit tests by @tsalo in https://github.com/PennLINC/aslprep/pull/221
  • Collect associated files at beginning of workflow by @tsalo in https://github.com/PennLINC/aslprep/pull/246
  • Refactor confounds and QC metrics by @tsalo in https://github.com/PennLINC/aslprep/pull/256

New Contributors

  • @tsalo made their first contribution in https://github.com/PennLINC/aslprep/pull/204
  • @josephmje made their first contribution in https://github.com/PennLINC/aslprep/pull/192

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.2.8...0.3.0

- Python
Published by tsalo almost 3 years ago

aslprep - compliance with paper

What's Changed

  • Sdcflow by @a3sha2 in https://github.com/PennLINC/aslprep/pull/144
  • Paper review by @a3sha2 in https://github.com/PennLINC/aslprep/pull/147
  • Paper review by @a3sha2 in https://github.com/PennLINC/aslprep/pull/148
  • update distortion correction by @a3sha2 in https://github.com/PennLINC/aslprep/pull/149
  • Update gecbf.py by @a3sha2 in https://github.com/PennLINC/aslprep/pull/150
  • Update setup.cfg by @a3sha2 in https://github.com/PennLINC/aslprep/pull/151
  • Paper review by @a3sha2 in https://github.com/PennLINC/aslprep/pull/152
  • Paper review by @a3sha2 in https://github.com/PennLINC/aslprep/pull/153
  • [skip ci] by @a3sha2 in https://github.com/PennLINC/aslprep/pull/154
  • [skip ci] by @a3sha2 in https://github.com/PennLINC/aslprep/pull/155
  • [skip ci] by @a3sha2 in https://github.com/PennLINC/aslprep/pull/156
  • Paper review by @a3sha2 in https://github.com/PennLINC/aslprep/pull/157
  • Paper review by @a3sha2 in https://github.com/PennLINC/aslprep/pull/158
  • quick start by @a3sha2 in https://github.com/PennLINC/aslprep/pull/159
  • update the boilerplate by @a3sha2 in https://github.com/PennLINC/aslprep/pull/160
  • Update quickstart.rst by @krmurtha in https://github.com/PennLINC/aslprep/pull/161
  • change the plotting parameters and units by @a3sha2 in https://github.com/PennLINC/aslprep/pull/162
  • Paper review by @a3sha2 in https://github.com/PennLINC/aslprep/pull/163
  • [skip ci] by @a3sha2 in https://github.com/PennLINC/aslprep/pull/164
  • df by @a3sha2 in https://github.com/PennLINC/aslprep/pull/165
  • edited quickstart.rst by @scovitz in https://github.com/PennLINC/aslprep/pull/166
  • Paper review by @a3sha2 in https://github.com/PennLINC/aslprep/pull/168
  • get tiscbf for PASL #167 by @a3sha2 in https://github.com/PennLINC/aslprep/pull/169
  • Issue 167 label duration pasl by @andrewrosss in https://github.com/PennLINC/aslprep/pull/170
  • Fix #171 by @andrewrosss in https://github.com/PennLINC/aslprep/pull/172
  • lower threshold mask by @a3sha2 in https://github.com/PennLINC/aslprep/pull/173

New Contributors

  • @scovitz made their first contribution in https://github.com/PennLINC/aslprep/pull/166
  • @andrewrosss made their first contribution in https://github.com/PennLINC/aslprep/pull/170

Full Changelog: https://github.com/PennLINC/aslprep/compare/0.2.7...0.2.8

- Python
Published by a3sha2 about 4 years ago

aslprep -

- Python
Published by a3sha2 almost 5 years ago

aslprep - bids validation

  • [x] bids validation is mandatory with bids-validator1.6.2 #135 #128
  • [x] inclusion of deltam, cbf #79 #82 #88 #80
  • [x] asl output space #111
  • [x] enhance visual reports

- Python
Published by a3sha2 almost 5 years ago

aslprep - testing

Add GE SCAN processing with deltam or cbf

suppressed freesurfer processing, FSL FLIRT with BBR for registration

basil and scorescrub as options, cbf computation is only default

- Python
Published by a3sha2 over 5 years ago

aslprep - testing stage

- Python
Published by a3sha2 over 5 years ago

aslprep - for testing

- Python
Published by a3sha2 over 5 years ago

aslprep - include sentry

- Python
Published by a3sha2 almost 6 years ago

aslprep - set for testing

- Python
Published by a3sha2 almost 6 years ago

aslprep - unstable release for testing

- Python
Published by a3sha2 almost 6 years ago