Nibabies

========================
This patch release includes a fix to FreeSurfer version detection, which was causing `recon-all` to use outdated flags.

========================
A bugfix release that includes missing files needed to run `infant_recon_all`.

Full Changelog
* FIX: Add missing shared object for `infant_recon_all` (231)
* RF: `migas` reporting (230)

=======================
A new minor release! The 22.1.x series of *NiBabies* includes:

- Improved alignment between FreeSurfer outputs and processed anatomical.
- Decreased memory usage while running across multiple processes (default).
- Fix to multi-echo processing in cases where an optimally combined file of all echoes was missing.
- Fix to the subcortical CIFTI to be in *LAS* orientation.

Full Changelog
* FIX: Correct fsnative <-> anatomical transforms (223)
* FIX: Vastly improve multi-echo handling (220)
* ENH: Add migas telemetry to nibabies (226)
* ENH: Add interface for reorienting images (229)
* DOCKER: Bump Python to 3.9 (221)
* RF/ENH: Rework workflow generation (219)

---------------------
A bug-fix release in the 22.0.x series.

This release includes a fix to a problem where `--cifti-output` was not
producing any outputs.

Full Changelog
* CI: Force all git-annex dependencies to be installed (217)
* CI: Simplify config with anchors (209)
* FIX: Remedy missing CIFTI outputs (212)
* MAINT: Set maximum scipy for Python 3.7.x (216)

----------------------
A bug-fix release in the 22.0.x series.

This release includes a fix for when using `UNCInfant` as an output space,
as well as a few improvements to susceptibility distortion correction (SDC).
These include a new flag (`--topup-max-vols`) for controlling the number of
volumes used by TOPUP, and support for SDC in the case where single phase-encoding
fieldmap is used to correct opposite phase-encoding BOLD/EPI runs.

Warning
This release includes a new version of PyBIDS, which now preserves any
zero-padding within the `run` entity. As a result, NiBabies output naming
may slightly differ from previous versions.

Full Changelog
* CI: Migrate to token auth when uploading to pypi (203)
* ENH: Improve fieldmap support (205)
* MAINT: Bump niworkflows (208)
* STY: Bump style dependencies, run isort on repo (206)

-----------------------
A new `NiBabies` minor series!

This release includes a number of new features, as well as various bug fixes. Some of the biggest changes include:
- [Ability to pass in anatomical derivatives](https://nibabies.readthedocs.io/en/latest/faqs.html#leveraging-precomputed-results).
Users can now leverage a precomputed brain mask and/or discrete anatomical segmentations.
- A new flag `--me-output-echoes` to output individual corrected echo time series.
This is useful when doing additional multi-echo processing.

Thank you for using *NiBabies*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

Full Changelog
* CI: Add workflow smoke tests (100)
* DOC: Add FAQs page (164)
* DOCKER: Upgrade to FSL6, use niprep miniconda base layer (191)
* ENH: Add major/minor version prefix to base workflow name (202)
* ENH: Add `--me-output-echos` CLI flag (174)
* ENH: Precomputed derivatives (173)
* ENH: Validate files passed with `--derivatives` (182)
* FIX: Clean up generated boilerplate (200)
* FIX: Various Configuration module touch-ups (197)
* FIX: Clean up default output space handling (196)
* FIX: Pandoc citeproc API incompatibility (195)
* FIX: Check if segmentation directory exists (165)
* FIX: Update report spec to reflect `infant_recon_all` (167)
* FIX: ICA Aroma imports (170)
* FIX: Relabel sub-structures before discarding (186)
* FIX: Use precomputed aseg within `infant_recon_all` (184)
* FIX: Remove excess arguments on wrapper tests (181)
* MAINT: Update versioneer, allow static versioning (190)
* MAINT: Ensure version is written to version file (189)
* MAINT: Add missing toml dependency
* MAINT: Add pre-commit checks (178)
* MAINT: Add RTD config (173)
* MAINT: Freeze `black` version (185)
* RF: Wrapper usage logic (183)
* STY/TEST: Set global style and doctest options (162)