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.

What's Changed

🛠 Breaking Changes

• Rename BIDS-noncompliant derivatives by @tsalo in #216
• Use correct bolus values in CBF calculation and temporarily disable Q2TIPS, multi-PLD, and no-BolusCutOff processing by @tsalo in #235
• Disable SCORE/SCRUB for GE/short runs and get GE workflow working by @tsalo in #248
• Parallelize parcellation and replace atlases by @tsalo in #254
• Remove "mean" from mean CBF filenames and add "timeseries" to 4D CBF filenames by @tsalo in #257

🎉 Exciting New Features

• Hardcode T1blood for some field strengths and use Zhang 2013 formula for others by @tsalo in #243
• Estimate labeling efficiency based on ASL type and number of background suppression pulses by @tsalo in #244

🐛 Bug Fixes

• Pin looseversion by @tsalo in #211
• Correct ordering of probseg maps by @josephmje in #192
• Convert inversion times to a list for compatility with BASIL interface by @tsalo in #222
• Pin networkx version by @tsalo in #227
• Use LabelingEfficiency as BASIL --alpha parameter by @tsalo in #233
• Remove BIDS-noncompliant m0z and cbf files by @tsalo in #236
• Replace RepetitionTime with RepetitionTimePreparation by @tsalo in #245
• Index aslcontext rows with "cbf", not "CBF" by @tsalo in #252

Other Changes

• Use aslprep_build as base Docker image - attempt 2 by @tsalo in #204
• Autoformat with black and isort by @tsalo in #205
• Replace relative imports with absolute ones by @tsalo in #206
• Remove unused functions and classes by @tsalo in #207
• Rename PEP8-noncompliant classes by @tsalo in #208
• Consistently use f-strings for string formatting by @tsalo in #209
• Work on fixing docstrings and splitting modules by @tsalo in #210
• Remove unused arguments throughout package by @tsalo in #212
• Replace smriprep calls with dependency calls by @tsalo in #217
• Replace pybids calls with dependency calls by @tsalo in #213
• Use custom formatting for workflow connections by @tsalo in #220
• Improve documentation by @tsalo in #218
• Add step to run unit tests by @tsalo in #221
• Collect associated files at beginning of workflow by @tsalo in #246
• Refactor confounds and QC metrics by @tsalo in #256

New Contributors

• @tsalo made their first contribution in #204
• @josephmje made their first contribution in #192

Full Changelog: 0.2.8...0.3.0

compliance with paper

What's Changed

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

New Contributors

• @scovitz made their first contribution in #166
• @andrewrosss made their first contribution in #170

Full Changelog: 0.2.7...0.2.8

0.2.8-beta: Merge pull request #144 from PennLINC/sdcflow

Sdcflow

bids validation

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

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

testing stage

0.2.5

Update setup.cfg

for testing

Merge pull request #11 from a3sha2/master

step plot for scoreindex

include sentry

0.2.1

Update .gitignore

set for testing

Merge pull request #9 from a3sha2/master

se

unstable release for testing

0.0.1

Update README.rst