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	_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.

🛠 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

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