What’s new
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 |
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Mean CBF |
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CBF time series after SCORE denoising |
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Mean CBF after SCORE denoising |
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Bolus arrival time/arterial transit time |
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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.
🛠 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/233Remove 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
0.2.7
Bids validation
0.2.6
11/12/2020
ENH - Add GE SCAN processing with deltam or cbf
ENH - supressed freesurfer processing, FSL FLIRT with BBR for registration
ENH - basil and scorescrub as options, cbf computation is only default