Fmriprep

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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)

==========================
New feature release in the 22.1.x series.

This is an incremental improvement on the 22.0.x series, including features and fixes that
are backwards incompatible with the 22.0.x work tree.

Several significant issues with susceptibility distortion correction (SDC) have been fixed
in `SDCFlows 2.2.0`_, in addition to the changes listed below.
If you have been seeing issues with SDC in 21.0.x or 22.0.x, please test out this version
and submit issues.

Additionally, this version includes improvements to structural preprocessing, generating
morphometric ``.shape.gii`` files from FreeSurfer derivatives.

Finally, this release introduces a method for estimating the carbon footprint of using
fMRIPrep. Add ``--track-carbon`` to your command to try this out. Note that it does not work
in Docker containers, but should work for Singularity containers.

With thanks to Nikhil Bhagwat for contributions.


* FIX: Conform --reports-only to match post-run report generation (2900)
* FIX: Remove cortex masking during vol2surf sampling (2879)
* FIX: Do not attempt to calculate TA if SliceTiming is degenerate (2901)
* FIX: Pass CrownCompCor components to GatherConfounds (2897)
* FIX: Output brain mask and boldref in BOLD space if individual echos requested (2852)
* FIX: Check for empty ACompCor results before trying to rename (2851)
* FIX: Filter sbrefs by BIDS filters if available (2843)
* ENH: Provide free memory estimate to unwarp_wf for better resources allocation (2910)
* ENH: Add migas telemetry in addition to sentry (2817)
* ENH: Tag memory based on data shape, annotate T2SMap (2898)
* ENH: Add of carbon tracker to estimate workflow emissions (2834)
* ENH: Output BOLD HMC transforms and reference volume (2860)
* RF: CIFTI generation (2884)
* DOC: Correct description of --longitudinal behavior (2905)
* MNT: Update fast track outputs, use latest smriprep (2894)
* MNT: Deprecate ``--topup-max-vols`` (2881)
* MNT: Add a ``--debug pdb`` to allow easier line-by-line debugging (2871)
* MNT: Generate more verbose reports (here, showing fieldmaps) if running in debug mode (2872)
* DOCKER: Build wheel and install in two-stage build (2859)
* CI: Various updates (2899)
* CI: Test on Python 3.10, bump actions versions (2895)
* CI: Fix non-fasttrack outputs for maint/21.0.x (2866)

===========================
A patch release in the 22.0.x series.

This release increases the minimum Nipype version to include better error messages on failures.
Additionally, this includes a fix to allow SyN distortion correction in combination with the
``--ignore fieldmaps`` option.

* MAINT: Add ``pre-commit``, dev installation for consistent styling (2857)
* CI: Upgrade docker orb (2858)