Fmriprep

======================

Bug fix release in the 23.1.x series.

In rare cases where Freesurfer is unable to align to its default atlas in
Talairach registration, it was unable to fall back to the Schwartz atlas
because we were not including it in the Docker image. This release exists
to provide an updated Docker image, and no upgrade is needed for users not
encountering this issue.

* DOCKER: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image (3049)

======================

Bug fix release in the 23.1.x series.

This release correctly generates ``*_space-fsLR_desc-reg_sphere.surf.gii``,
which was previously a copy of the standard ``*_desc-reg_sphere.surf.gii``.
Additionally, warnings are now correctly emitted when AROMA-related CLI
options are used.

* CI: Clean up pre-release builds (3040)

======================

Bug fix release in the 23.1.x series.

This release corrects a small error that prevented the "goodvoxels" mask from
being placed in the output directory if no FreeSurfer output spaces were specified.

* FIX: Remove bad metadata input from ds_goodvoxels_mask (3037)

======================
New feature release in the 23.1.x series.

This release substantially reworks the resampling to fsLR grayordinate space,
better accounting for partial volumes and high variance voxels. If you are
resampling using ``--project-goodvoxels``, we strongly recommend upgrading.

Fieldmap handling is improved, with better preference given to single-band
references in both PEPolar and SyN-SDC schemes. Additionally, fMRIPrep will
no longer estimate fieldmaps that are not intended to be used to correct BOLD
series, reducing unneeded processing.

This release removes ICA-AROMA from the fMRIPrep workflow. To use ICA-AROMA,
set ``MNI152NLin6Asym:res-2`` as a target output space. MELODIC and ICA-AROMA
can be run on the resulting images in a separate pipeline. For further
information on the reasoning behind this change, see
`GitHub issue 2936 <https://github.com/nipreps/fmriprep/issues/2936>`__.

This release increments the versions of ANTs and FSL bundled in the Docker
image.

With thanks to Eilidh MacNicol, Basille Pinsard and Taylor Salo for contributions
in fMRIPrep and SDCflows.

* FIX: Raise RuntimeError at build if echos have mismatched shapes (3028)
* FIX: Inconsistent fmapless estimation when ignoring fieldmaps (2994)
* FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (2986)
* FIX: Estimate free memory with "available", not "free" (2985)
* ENH: Add ``--me-t2s-fit-method`` parameter (3030)
* ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (3011)
* ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (3008)
* ENH: Remove ICA-AROMA from workflow and docs (2966)
* RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (3025)
* MNT: Update ANTs pin in Docker image (3016)
* MNT: Update governance docs (2992)
* MNT: Refactor Docker build process (2982)
* MNT: Pin conda environment more strictly (2853)
* MNT: Require niworkflows ~1.3.6 (2740)
* CI: Use registry for layer caching (3012)
* CI: Upgrade docker orb (2865)

=======================
Bug fix release in the 23.0.x series.

This release fixes issues with `_phase1+2`, `_phasediff` and `_fieldmap`
fieldmap files that are found with an orientation other than RAS.

=======================
Bug fix release in the 23.0.x series.

This release fixes issues with detecting partial fieldmaps, emitting a warning instead
of an error. A small change in sMRIPrep fixes the name of a workflow, which may cause a
duplication in a reused work directory from 23.0.0, but should not break any workflows
or produce a change in derivatives.