Smriprep

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New feature release in the 0.14.x series.

This release restores correct handling of cohort identifiers in templates.
A feature release is warranted due to changes in the workflow structure.

* FIX: Fetch templates during workflow construction (418)
* FIX: Re-add cohort identifier to template name (416)
* FIX: Repair FreeSurfer Dependency in Dockerfile (tcsh) (404)
* FIX: Invert result of skull-strip check in auto mode (402)
* STY: Adopt ruff for linting and formatting (397)
* CHORE: Update ruff, ignore certain rules (419)

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Bug fix release in the 0.13.x series.

This release fixes a check for skull-stripping in auto mode, and adds
missing fsLR atlases to the Python package resources.
The Docker image has also been updated to ensure FreeSurfer can be run
from the sMRIPrep container.

With thanks to Patrick Sadil for reports and fixes.

* ENH: Add 59k atlases (405)
* FIX: Repair FreeSurfer dependency in Dockerfile (tcsh) (404)
* FIX: Invert result of skull-strip check in auto mode (402)

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Bug fix release in the 0.13.x series.

This release fixes a bug with a workflow connection that was not properly
named, and which would cause an error when T2-weighted images were provided.

* FIX: T1w_preproc -> t1w_preproc (399)

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New feature release in the 0.13.x series.

This release adds support for MSM-Sulc, improving the alignment of subject
surfaces to the fsLR template. This process is enabled by default, but may
be disabled with the ``--no-msm`` flag.

The ``--fast-track`` flag has been deprecated in favor of a more flexible
``--derivatives`` flag. This flag can be used to specify one or more
directories to search for derivatives. Derivatives found in these
directories can be used to skip corresponding workflows. For derivatives
that can be deterministically generated from other derivatives, sMRIPrep
will regenerate the derivatives to avoid inconsistencies.

This supports the 23.2.x series of fMRIPrep, which introduces a ``--level``
flag to control the level of processing. This feature is not currently
available in sMRIPrep, but will be in a future release. To preview this
functionality, use fMRIPrep's ``--anat-only`` flag to run only structural
workflows.

* FIX: Add missing fsLR reg sphere to io_spec (382)
* FIX: Invert sulcal depth metric before passing to MSM, use HCP atlas files (383)
* FIX: Update surfaces with fsnative2t1w_xfm (384)
* FIX: Add surface-modify-sphere call to catch potential sphere elongation (375)
* ENH: Add T2w/FLAIR usage to boilerplate (392)
* ENH: Annotate mris_expand with thread usage (386)
* ENH: Add sphere registration to fit workflow, check for precomputed (370)
* ENH: Save msm registration sphere as desc-msm_sphere.surf.gii (365)
* ENH: Add Multimodal Surface Matching (358)
* ENH: Run pytest on CircleCI (364)
* ENH: Separate surfaces and morphometrics into standalone outputs (359)
* RF: Split template and fsLR resampling and sinking into isolated workflows (388)
* RF: Replace most of anat_ribbon_wf with a Python function (363)
* RF: Break up surface workflows for easier mix-and-match in fMRIPrep (360)
* TEST: Add smoke tests for main anatomical workflows (390)
* TEST: Add sloppy MSM configuration for use in debugging/CI (366)
* DOC: http:// → https:// (#377)
* DOC: Fix misspelling found by codespell (378)
* MNT: Remove AFNI from smriprep docker container (387)
* MNT: Use a set literal, not a list literal (379)
* MNT: Update installation environment (361)
* MNT: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image (357)
* MNT: Infrastructure updates (351)
* MNT: fix flake8 warning (349)
* MNT: apply pyupgrade suggestions (348)
* MNT: fix typos found by codespell (346)
* MNT: Python 3.11 should be supported (347)

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Bug-fix release in the 0.12.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 (357)

======================
Bug-fix release in the 0.12.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``.

* FIX: Pass sphere_reg_fsLR to ds_reg_fsLR (350)