Nibabies

---------------------
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)

--------------------------
A patch release in the 21.0.x series.
This release removes the 24 month age cap for infant recon all processing, as well as includes various small maintenance fixes.

Full Changelog
* DOC: Use dynamic versioning for examples (151)
* ENH: Remove infant recon all age cap (154)
* FIX: Generate boilerplate (157)
* FIX: Avoid requiring service when checking wrapper version (159)
* MAINT: Fix dirty version on release (144)
* MAINT: Only alter pybids config in legacy versions (152)
* MAINT: Prefetch neonate MNIInfant templates (159)
* MAINT: Update git-annex version (159)
* RF: Initialize BIDSLayout with dedicated indexer (146)

-------------------------
A patch release in the 21.0.x series.

This patch release is for all **Docker/Singularity** users: `infant_recon_all` did not have all the available templates, which would cause failures for certain ages.
Upgrading to this release will ensure you have all the necessary templates.

Full Changelog
* DOCKER: Add missing `infant_recon_all` templates (130dcf3)

-------------------------
The first major release series of 2021.

This release includes enhancements, such as:
- Fine-grain subcortical alignment during CIFTI generation
- Improved functional registration to template space
- Greatly minimized container environment

Additionally, a plethora of bug-fixes are included, and documentation has been improved.

Caution!
As with all minor version increments, working directories from previous versions **should not be reused**.

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!


Full Changelog
* DOC: Set up external readthedocs documentation (119) (126) (128)
* DOCKER: Reduce container image size (105) (133)
* DOCKER: Strip ABI tag from libQt5Core.so.5 (109)
* DOCKER: Modernize Dockerfile (85)
* ENH: Port slice timing correction enhancements from fMRIPrep (137)
* ENH: Change default `--output-layout` to bids (130)
* ENH: Subcortical alignment workflow (72)
* ENH: Framewise displacement head radius flag (104)
* ENH: Incorporate subcortical CIFTI alignment to functional processing (102)
* ENH: Do not run infant_recon_all if already completed (101)
* FIX: Handle sessions when grouping BOLDs (139)
* FIX: Ensure MNIInfant is added if no `--output-spaces` are used (136)
* FIX: Ensure `nibabies-wrapper` patches are correctly bound (113)
* FIX: BOLD to template normalization (99)
* FIX: SDC fieldwarp application (98)
* FIX: Avoid running BBReg under certain conditions (95)
* FIX: Standard output spaces (92)
* FIX: Small Docker environment fixes (86)
* FIX: Feed NiTransforms with LTAs of type RAS2RAS (84)
* MAINT: Rename default `infant_recon_all` output directory (129)
* MAINT: Bump SDCFlows to latest bugfix version (d799fee)
* MAINT: Attempt to pull most recent dev version (94)
* MAINT: Initial CircleCI workflow (93)
* STY: `black` nibabies module (118)