Qsiprep

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

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

Please note there is no corresponding release on PyPI for this version

New features

* [ENH] allow topup+drbuddi for hbcd by mattcieslak in https://github.com/PennLINC/qsiprep/pull/667
* Adds a 2-stage distortion correction option `--pepolar-method TOPUP+DRBUDDI`, which will run TOPUP -> Eddy -> DRBUDDI
* [ENH] Use UKB processed data as input for recon workflows by mattcieslak in https://github.com/PennLINC/qsiprep/pull/651
* This adds the --recon-input-pipeline, which lets you run recon workflows on UKB data
* [ENH] Update to python 3.10 by mattcieslak in https://github.com/PennLINC/qsiprep/pull/670
* Hopefully this will address the hang-after-crashing problem in the recent releases

Bugfixes/Docs

* DOC: Add SMeisler and JHLegarreta to contributors list by jhlegarreta in https://github.com/PennLINC/qsiprep/pull/642
* Fixes typos on FreeSurfer requirements for ss3t hsvs recon by pcamach2 in https://github.com/PennLINC/qsiprep/pull/414
* Fix RTD build by tsalo in https://github.com/PennLINC/qsiprep/pull/652
* ENH: conform bvals to shells separated by b0_threshold by cookpa in https://github.com/PennLINC/qsiprep/pull/660
* [FIX] remove unneeded "method" from tracking by mattcieslak in https://github.com/PennLINC/qsiprep/pull/641
* FIX: allow finding of lesion rois by psadil in https://github.com/PennLINC/qsiprep/pull/659
* MISC: Remove outdated dsi_studio tracking parameters by cookpa in https://github.com/PennLINC/qsiprep/pull/668
* [DOC] Add documentation for dsi_studio_autotrack reconstruction workflow by valeriejill in https://github.com/PennLINC/qsiprep/pull/669
* [ENH] Update BIDS validator to 1.8.4 by mattcieslak in https://github.com/PennLINC/qsiprep/pull/671

Addresses stability issues in the 0.18 releases. Huge improvements to AutoTrack recon workflow
CPU use and improvements in memory use for synthseg and synthstrip

* [ENH] limit the synths to 1 thread (608)
* [DOC] fix typo in docs (606)
* [ENH] Stabilize autotrack performance (604)
* [CI] Add test for tensor-based head motion correction (605)
* [FIX] fixes steinhardt computation (603)

No technical changes to the pipeline here, but citations and methods boilerplate have been updated to
reflect the changes in 0.18.0alpha0.

First release moving towards 1.0! Please open bug reports if anything suspicious comes up. This release
changes the anatomical workflow significantly, synthstrip and synthseg are used. The recon workflow
"dsi_studio_autotrack" has also been added.

What's Changed

* Bump sentry-sdk from 0.13.1 to 1.14.0 by dependabot in https://github.com/PennLINC/qsiprep/pull/539
* [ENH] Update FreeSurfer to 7.3.1, dmri-amico to 1.5.4 by mattcieslak in https://github.com/PennLINC/qsiprep/pull/537
* WIP: ENH: Make pyAFQ tests faster, add export all by 36000 in https://github.com/PennLINC/qsiprep/pull/534
* [ENH] move biascorrect so it runs on resampled data by default by mattcieslak in https://github.com/PennLINC/qsiprep/pull/527
* [Fix] Fix threading on DRBUDDI interface by mattcieslak in https://github.com/PennLINC/qsiprep/pull/540
* [ENH] add CNR to the imageqc.csv by mattcieslak in https://github.com/PennLINC/qsiprep/pull/541
* [FIX] pin pandas version to < 2.0.0 by mattcieslak in https://github.com/PennLINC/qsiprep/pull/543
* ENH: Replace avscale with non-fsl tools by jbh1091 in https://github.com/PennLINC/qsiprep/pull/542
* ENH: Replace fsl applymask by jbh1091 in https://github.com/PennLINC/qsiprep/pull/544
* Replace fsl split by jbh1091 in https://github.com/PennLINC/qsiprep/pull/548
* [FIX] Update distortion_group_merge.py by smeisler in https://github.com/PennLINC/qsiprep/pull/555
* [ENH] Redo anatomical workflow by mattcieslak in https://github.com/PennLINC/qsiprep/pull/553
* [FIX] remove pre bids-filter acq type argument by octomike in https://github.com/PennLINC/qsiprep/pull/557
* FIX: Replace deprecated `np.int` instances by smeisler in https://github.com/PennLINC/qsiprep/pull/558
* [WIP] ENH: 482 remove fsl dependency by jbh1091 in https://github.com/PennLINC/qsiprep/pull/498
* [ENH] Update TORTOISE for improved T2w registration by mattcieslak in https://github.com/PennLINC/qsiprep/pull/564
* [FIX] T2w anat-modality issues by mattcieslak in https://github.com/PennLINC/qsiprep/pull/565
* [FIX] update boost in tortoise by mattcieslak in https://github.com/PennLINC/qsiprep/pull/569
* [FIX] connections on multi-anat workflow by mattcieslak in https://github.com/PennLINC/qsiprep/pull/572
* [ENH] Update DSI Studio to the latest commit by mattcieslak in https://github.com/PennLINC/qsiprep/pull/573
* [ENH] Add DSI Studio AutoTrack recon workflow by mattcieslak in https://github.com/PennLINC/qsiprep/pull/576

New Contributors
* dependabot made their first contribution in https://github.com/PennLINC/qsiprep/pull/539
* jbh1091 made their first contribution in https://github.com/PennLINC/qsiprep/pull/542
* smeisler made their first contribution in https://github.com/PennLINC/qsiprep/pull/555

**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.17.0...0.18.0alpha0