What’s new
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
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 |
|
|
Mean CBF |
|
|
CBF time series after SCORE denoising |
|
|
Mean CBF after SCORE denoising |
|
|
Bolus arrival time/arterial transit time |
|
|
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