Fmriprep

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

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.

=======================
New feature release in the 23.0.x series.

This release adds improvements for workflows targeting the fsLR grayordinate space.
Namely, morphometric (curvature, sulcal depth and cortical thickness) measures are
output as ``.dscalar.nii`` files and high-variance voxels can be excluded from the
resampling step using ``--project-goodvoxels``.

Additionally, T2w images are now resampled to the T1w-defined subject space if FreeSurfer
reconstruction is used. If multiple T2w images are provided, they are merged into a single
image first.

PEPolar fieldmaps with R/L phase-encoding directions or in non-standard orientations
are now better supported. We continue to work toward better support for more SDC
configurations.

23.0.0 supports FreeSurfer 7.3.2, which is now bundled in the Docker image.

ICA-AROMA support will be removed in 23.1.0.

With thanks to Thomas Madison, Greg Conan, Celine Provins, Robert Smith and Yaroslav
Halchenko for contributions.
Thanks also to Steve Giavasis and colleagues at the Child Mind Institute
for feedback on SDC processing.

* FIX: Pass reference image to unwarp_wf, use reference fieldwarp for single shot (2945)
* FIX: Pass fmap filters to sdcflows (2932)
* ENH: Resample morphometrics to fsLR dscalar CIFTI-2 files if ``--cifti-output`` is used (2959)
* ENH: Add option to exclude projecting high variance voxels to surface (update of 2855) (2956)
* ENH: Separate deep from shallow WM+CSF in the carpetplot (2744)
* ENH: Merge T2w images and coregister to T1w template (2941)
* RF: Use DataFrame.rename instead of ad hoc process (2937)
* DOC: Update the description of the carpetplot in the sample report (2950)
* DOC: Altered CLI option grouping (2944)
* DOC: Update lesion ROI documentation, warn in docs and app about upcoming changes (2943)
* DOC: Update docs following read-through (2930)
* DOC: Update carpetplot in "Outputs of fMRIPrep" (2923)
* MNT: Codespell config, action + some typo fixups (2958)
* MNT: Warn that AROMA support will be removed in a future version (2940)
* MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D (2931)
* MNT: Switch to hatch build backend and update package metadata (2914 + 2939)
* MNT: Rotate CircleCI secrets and setup up org-level context (2928)
* CI: Minor updates to CircleCI config to improve resilience (2957)
* CI: Weekly docker build from scratch (2938)

=========================
Bug fix release in the 22.1.x series.

This release fixes the reported version in the distributed Docker image,
and depends on SDCFlows 2.2.2, which fixes a bug affecting SDC estimation
in some oblique datasets.

* FIX: Ensure version installed in Docker file is clean (2922)