0.18.0 (May 08, 2025)

New feature release in the 0.18.x series.

This release patches the FSL FAST interface to disable bias field correction,
which is redundant with N4 and can cause problems in some populations.

* FIX: Respect label order in precomputed derivatives (#478)
* FIX: Set FAST bias_iters parameter to 0 (#472)
* ENH: Tag structural workflows (#476)
* MNT: Update pinned environment, use conda-forge connectome-workbench (#468)

0.17.0 (December 19, 2024)

New feature release in the 0.17.x series.

This release improves handling of datasets where T1w images are not
the primary modality. It also supports the generation of fsLR meshes
on the subject surface with the names:

    sub-<label>/anat/sub-<label>_hemi-<L|R>_space-fsLR_den-<label>_<surface>.surf.gii

These are useful for plotting CIFTI results on subject anatomy.

* FIX: Stop excluding FS minc_modify_header used during fallback registration (#453)
* ENH: Output fsLR meshes on subject surfaces (#460)
* ENH: Support spatial normalization to alternative modalities (#459)
* ENH: Add `t2w_file` output to `TemplateFlowSelect` (#457)
* MNT: Enable pre-release tests (#461)
* MNT: Complete transition from flake8/black to ruff (#435)
* MNT: Adopt src/ layout and tox (#458)

0.16.1 (August 26, 2024)

A bug-fix release that reworks selection within the
FreeSurfer to native segmentation resampling workflow.

* FIX: Select function in segmentation resampling workflow (#450)

0.16.0 (July 31, 2024)

Start of the 0.16.x minor series.

This release decouples much of the hardcoded T1w behavior in favor of T1w/T2w options,
to allow easier integration with tools less reliant on a single anatomical scan.

* ENH: Use genericised "anat" input/output for TemplateDimensions (#443)
* ENH: Remove much of the hardcoded `T1w` fields in favor of `anat` (#433)
* RF: Load package data with acres (#448)
* RF: `space-fsaverage` to `sphere_reg` output files (#446)
* MNT: Unpin libitk 5.3 (ANTs 2.5.3 is built with 5.4) (#445)
* MNT: Clean up doc builds, environment, style checks (#444)

0.15.0 (March 22, 2024)

New feature release in the 0.15.x series.

This release adds the workflow configuration option and CLI option
to reuse existing FreeSurfer outputs without attempting to resume.
This should allow for using longitudinal or non-standard pipelines
(for example, FastSurfer) without additional tooling for each variant.

* FIX: Patch version for smriprep-docker (#424)
* FIX: Require recent templateflow, select correct aparc dseg.tsv (#420)
* ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#393)
* MNT: set copyright owner in LICENSE file (#426)
* MNT: Apply Repo-Review suggestions (#422)
* CI: Small cleanups to GHA (#423)

0.14.0 (March 11, 2024)

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)

0.13.2 (December 08, 2023)

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)

0.13.1 (November 21, 2023)

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)

0.13.0 (November 20, 2023)

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)

0.12.2 (August 16, 2023)

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)