Qsiprep

This is a prerelease for the version that will be used by the HBCD project for their first data release.
Starting with this release, QSIPrep is now being deployed to `pennlinc/qsiprep`
on DockerHub instead of `pennbbl/qsiprep`.

We plan to not introduce any backwards-incompatible changes for a while.

<!-- Release notes generated using configuration in .github/release.yml at master -->

What's Changed

🛠 Breaking Changes

* Replace pennbbl with pennlinc in package by tsalo in https://github.com/PennLINC/qsiprep/pull/869
* Move common metadata to top of JSON by tsalo in https://github.com/PennLINC/qsiprep/pull/875

🐛 Bug Fixes

* [FIX] synthstrip extra arg by mattcieslak in https://github.com/PennLINC/qsiprep/pull/881
* Pin nireports version and allow GIFs by tsalo in https://github.com/PennLINC/qsiprep/pull/883

Other Changes

* Restructure documentation and document how to run tests locally by tsalo in https://github.com/PennLINC/qsiprep/pull/879


**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.24.0...1.0.0rc1

<!-- Release notes generated using configuration in .github/release.yml at 0.24.0 -->

What's Changed
🛠 Breaking Changes
* Rename `--anat-space-definition` to `--subject-anatomical-reference` by tsalo in https://github.com/PennLINC/qsiprep/pull/855
* Remove underscore versions of all parameters by tsalo in https://github.com/PennLINC/qsiprep/pull/861
* Change T1wACPC to ACPC and T1wNative to anat by tsalo in https://github.com/PennLINC/qsiprep/pull/859
* Change _cnr to stat-cnr_dwimap by tsalo in https://github.com/PennLINC/qsiprep/pull/867
* Rename confounds file to `desc-confounds_timeseries` by tsalo in https://github.com/PennLINC/qsiprep/pull/874
🎉 Exciting New Features
* Infer the appropriate MNIInfant cohort based on the participant's age by tsalo in https://github.com/PennLINC/qsiprep/pull/856
* Make grouping account for acquisition entity by tsalo in https://github.com/PennLINC/qsiprep/pull/862
🐛 Bug Fixes
* [FIX] Change to Linear for upsampling by mattcieslak in https://github.com/PennLINC/qsiprep/pull/820
* Add MNIInfant to template enum by tsalo in https://github.com/PennLINC/qsiprep/pull/824
* Add ability to ignore phase data by tsalo in https://github.com/PennLINC/qsiprep/pull/849
* Use correct base name with `--distortion-group-merge average` by tsalo in https://github.com/PennLINC/qsiprep/pull/863
Other Changes
* [CI] Swap synthstrip for bet when sloppy mode is chosen by mattcieslak in https://github.com/PennLINC/qsiprep/pull/817
* [FIX] Constrain threading for intramodal template by mattcieslak in https://github.com/PennLINC/qsiprep/pull/825
* [FIX] use correct arguments for merging distortion groups by mattcieslak in https://github.com/PennLINC/qsiprep/pull/831
* rf(py314): Replace deprecated pkgutil.find_loader by effigies in https://github.com/PennLINC/qsiprep/pull/828
* [ENH] Enable session selection by mattcieslak in https://github.com/PennLINC/qsiprep/pull/832
* [FIX] Add denoising reportlets back to html by mattcieslak in https://github.com/PennLINC/qsiprep/pull/841
* [ENH] Add derivatives metadata by mattcieslak in https://github.com/PennLINC/qsiprep/pull/844
* Use "Apptainer" instead of "Singularity" by arokem in https://github.com/PennLINC/qsiprep/pull/846
* Document the transforms produced by QSIPrep by tsalo in https://github.com/PennLINC/qsiprep/pull/866
* Add warning for pennbbl Docker image by tsalo in https://github.com/PennLINC/qsiprep/pull/870
* Add QSIPrep paper to boilerplate by tsalo in https://github.com/PennLINC/qsiprep/pull/873
* Remove `aggr_ses_reports` field by tsalo in https://github.com/PennLINC/qsiprep/pull/872

New Contributors
* effigies made their first contribution in https://github.com/PennLINC/qsiprep/pull/828

**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.23.0...0.24.0

<!-- Release notes generated using configuration in .github/release.yml at 0.22.0 -->
A huge number of infrastructure upgrades to improve testing and test coverage. An update to PyAFQ! Also a number of bug fixes, including for the hsvs recon workflows

What's Changed
🐛 Bug Fixes
* Fix FUGUE bug by tsalo in https://github.com/PennLINC/qsiprep/pull/769
Other Changes
* [ENH] Update to NiPreps-style config file by mattcieslak in https://github.com/PennLINC/qsiprep/pull/745
* Fix API documentation by tsalo in https://github.com/PennLINC/qsiprep/pull/748
* Run integration tests with pytest by tsalo in https://github.com/PennLINC/qsiprep/pull/763
* MAINT: Upgrade pyAFQ to 1.3.2 by arokem in https://github.com/PennLINC/qsiprep/pull/764
* [ENH] Update dependencies in docker image by mattcieslak in https://github.com/PennLINC/qsiprep/pull/768
* [CI] add optional bundles by mattcieslak in https://github.com/PennLINC/qsiprep/pull/771
* [FIX] Fix the mif2fib workflow by mattcieslak in https://github.com/PennLINC/qsiprep/pull/778
* Save SIFT2 mu parameter by araikes in https://github.com/PennLINC/qsiprep/pull/774
* Drop functions to read sidecar JSONs by tsalo in https://github.com/PennLINC/qsiprep/pull/760
* [FIX] Use new bundle names by mattcieslak in https://github.com/PennLINC/qsiprep/pull/783
* [FIX] Make hsvs workflow work by mattcieslak in https://github.com/PennLINC/qsiprep/pull/784
* [ENH] Compress recon derivatives by mattcieslak in https://github.com/PennLINC/qsiprep/pull/787

New Contributors
* araikes made their first contribution in https://github.com/PennLINC/qsiprep/pull/774

**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.21.4...0.22.0

<!-- Release notes generated using configuration in .github/release.yml at 0.21.4 -->

What's Changed
The effort to update to current NiPreps standards has begun, plus another bugfix in the TOPUP workflow.

Other Changes
* Remove copy of Niworkflows in favor of dependency by tsalo in https://github.com/PennLINC/qsiprep/pull/709
* [FIX] stop bizarre argsort behavior in best b=0 by mattcieslak in https://github.com/PennLINC/qsiprep/pull/744


**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.21.3...0.21.4

<!-- Release notes generated using configuration in .github/release.yml at 0.21.3 -->

What's Changed

This update addresses an important coregistration bug (740), makes CPU Eddy much more usable and fixes a bug in the PyAFQ workflow.

Other Changes
* [FIX] PyAFQ was not being written to derivatives by mattcieslak in https://github.com/PennLINC/qsiprep/pull/738
* [FIX] use b0 ref from eddy-processed data by mattcieslak in https://github.com/PennLINC/qsiprep/pull/739
* [MAINT] remove pypi by mattcieslak in https://github.com/PennLINC/qsiprep/pull/742
* [ENH] add parallel argument for topup by mattcieslak in https://github.com/PennLINC/qsiprep/pull/741
* [ENH] Allow multithreading in eddy by mattcieslak in https://github.com/PennLINC/qsiprep/pull/743


**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.21.1...0.21.3

What's Changed

There are important software updates in this release, along with a lot of infrastructure improvements.

Important Changes
* FSL version 6.0.7.8 is now in qsiprep. This contains 2 [serious bugfixes](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/development/history/changelog-6.0.7.8.md). One has to do with susceptibility-by-volume correction and the other resulted in incorrect CNR values being calculated.
* DSI Studio has been updated to fix a bug in [Neighboring DWI Correlation](https://github.com/frankyeh/DSI-Studio/issues/84).
* You can use `"mporder"` in your eddy config json file and the slice timings will automatically be created and passed to eddy (even if you're concatenating runs)
* Recon workflows can now include a "bundle mapping" and "scalar mapping", where scalars created in individual workflows can be mapped to a template or summarized inside autotrack bundles. This does not do tract profiles or surface mapping - yet. See `qsiprep/data/pipelines/hbcd_scalar_maps.json` for an example.
* The recon derivatives are written approximately according to BEP-016

🎉 Exciting New Features

* [ENH] Add workflow to resample recon scalars to template space by mattcieslak in https://github.com/PennLINC/qsiprep/pull/688
* Support complex-valued dwidenoising by tsalo in https://github.com/PennLINC/qsiprep/pull/679
* [ENH] Add ReconScalars node to recon workflows by mattcieslak in https://github.com/PennLINC/qsiprep/pull/683
* Pin current version of pyAFQ (1.3.1) by arokem in https://github.com/PennLINC/qsiprep/pull/729
* [ENH] Add TORTOISE Estimator recon workflows by mattcieslak in https://github.com/PennLINC/qsiprep/pull/674
* [ENH] Make Eddy's slice2vol much easier to use by mattcieslak in https://github.com/PennLINC/qsiprep/pull/710

Other Changes
* Apply stylistic changes to `workflows/base.py` by tsalo in https://github.com/PennLINC/qsiprep/pull/678
* Pin Nilearn version by tsalo in https://github.com/PennLINC/qsiprep/pull/687
* Add a series of infrastructure files from ASLPrep/XCP-D by tsalo in https://github.com/PennLINC/qsiprep/pull/684
* Run isort and remove unused imports by tsalo in https://github.com/PennLINC/qsiprep/pull/690
* Apply stylistic changes to `workflows/utils.py` by tsalo in https://github.com/PennLINC/qsiprep/pull/680
* Remove unused classes flagged by vulture by tsalo in https://github.com/PennLINC/qsiprep/pull/693
* [RF] Use Black to reformat package by mattcieslak in https://github.com/PennLINC/qsiprep/pull/701

Bugfixes
* [FIX] Prevent undecodable terminal output in calc_connectivity by mattcieslak in https://github.com/PennLINC/qsiprep/pull/711
* [FIX] save recon anat files by mattcieslak in https://github.com/PennLINC/qsiprep/pull/702
* [FIX] revert citeproc for old pandoc by mattcieslak in https://github.com/PennLINC/qsiprep/pull/736
* [FIX] recon workflows when --anat-modality T2w was used by mattcieslak in https://github.com/PennLINC/qsiprep/pull/734
* [FIX] remove old nodes from csdsi_3dshore.json by kjamison in https://github.com/PennLINC/qsiprep/pull/733
* [ENH] Update TORTOISE for lower cuda memory use by mattcieslak in https://github.com/PennLINC/qsiprep/pull/730

New Contributors
* kjamison made their first contribution in https://github.com/PennLINC/qsiprep/pull/733

**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.20.0...0.21.1