2.13.1 (Jane 12, 2025)

Patch release in the 2.13.x series.

This includes a fix to ``init_fmap_preproc_wf`` node naming.

* FIX: Use the sanitized id when naming through nipype (#495)

2.13.0 (May 15, 2025)

Feature release in the 2.13.x series.

This release addresses some longstanding issues with the SyN-SDC workflow,
improving the registration quality in adult humans by utilizing a spatial prior,
as well as allowing Laplacians to be up- or down-weighted in the cost function,
making it more usable across species.

Additionally, this release allows for the use of ``EstimatedTotalReadoutTime`` or
``EstimatedEchoSpacing``, or a manually provided fallback ``TotalReadoutTime`` value,
permitting the use of SDCFlows on datasets that do not have reliable timing information
without introducing incorrect metadata into the datasets.

* fix(syn): Re-enable priors respecting ``sd_priors`` argument (#488)
* feat: Add workflow arguments for metadata estimates and fallback TRT (#479)
* feat(syn): Update totalFieldVarianceInVoxel space based on voxel resolution (#487)
* feat(syn): Allow changing laplacians weights in SyN registration metric (#484)
* test(syn): Add a test to exercise SyN workflow creation and check parameters (#486)

2.12.0 (March 21, 2025)

Feature release in the 2.12.x series.

This release migrates from the deprecated ``niworkflows.reporting``
module to the ``nireports`` package.

* FIX: AttributeError for _ApplyCoeffsFieldInputSpec (#481)
* ENH: Allow running SyN SDC without using prior (#480)
* ENH: Allow estimated and fallback TotalReadoutTime (#477)
* RF: Transition from niworkflows reporting interfaces (#473)
* DOC: Fix broken link [skip ci] (#482)
* MNT: Add `defaults` to `conda` channels in `build-test-publish` GHA (#474)
* MNT: Update `niworkflows` version to 1.11.0 (#478)

2.11.0 (December 18, 2024)

Feature release in the 2.11.x series.

This release supports numpy 2 and Python 3.13.

* FIX: Normalize BIDS-URIs to subject-relative (#458)
* FIX: Only fit high-frequency spline for SyN-SDC (#457)
* ENH: Allow Jacobian correction to be toggled on/off (#462)
* ENH: Dilate fmap and bold masks during coregistration (#463)
* TEST: Clear registry consistently to avoid order dependency (#464)
* DOC: Plot correct workflow in init_syn_preprocessing_wf docstring (#460)
* CI: Drop CircleCI, using GHA only (#459)

2.10.0

Feature release in the 2.10.x series.

The main change is a bugfix when fitting multi-level B-Splines to some
noisy fieldmaps.
The multi-level fitting, while being theoretically nice, does not really
bring anything immediately as we are not generally inverting the distortion.
In this release, the default fitting has been change to single-level B-Splines,
with a spacing similar to TOPUP's defaults.

With thanks to Sunjae Shim (@sjshim) for sharing Spiral-echo fieldmaps that
were failing prior the patch in #453.

CHANGES
-------

* FIX: Revision of the B-Spline fitting code (#453)
* FIX: Building Docker image on ARM64 devices (#449)
* ENH: Improve plots in jupyter notebook (#452)
* DOC: Fix ``ValueError`` in notebook's output. (#450)

2.9.0 (June 13, 2024)

Feature release in the 2.9.x series.

The main change is that B0FieldIdentifiers with special characters
are now sanitized and exposed through a ``FieldmapEstimator.sanitized_id``
attribute.

Workflow names and input/output connections will use ``sanitized_id``,
to ensure compatibility with filenames and workflow graph generation.
Internal lookup tables will continue to use the the unsanitized ``bids_id``.

* FIX: Update suffix only when finding related fieldmap files (#436)
* FIX: Remove unused ANTs parameter that was removed in 2.4.1 (#431)
* RF: Add sanitized_id field to FieldmapEstimation (#444)
* DOC: Un-mock the already-imported numpy (#440)
* CI: Bump actions/cache from 3 to 4 (#429)

1.3.5 (February 14, 2024)

Bug-fix release in 1.3.x series.

* FIX: Remove unused ANTs parameter that was removed in 2.4.1 (#431)

2.8.1 (January 22, 2024)

Bug-fix release in the 2.8.x series.

Fixes doc builds and CLI support for fieldmapless workflows.
Introduces support for BIDS-URIs.

* FIX: Enable fieldmapless by default in CLI (#426)
* FIX: Pandoc requires Texlive to render LaTeX in notebook (#427)
* FIX: New test ``test_wrangler_URIs`` had the wrong oracle (#425)
* ENH: Resolve BIDS-URIs (#349)
* TEST: Use less confusing function name for testing CLI with --dry-run (#424)
* MNT: Bump actions/download-artifact from 3 to 4 (#418)
* MNT: Bump actions/upload-artifact from 3 to 4 (#417)
* CI: Move PR doc build into main doc build, add texlive to build dependencies (#428)

2.8.0 (January 10, 2024)

New feature release in the 2.8.0 series.

This release fixes a bug in converting SyN-SDC displacements to fieldmaps,
resulting in exaggerated corrections. As this makes changes to the structure
of a workflow and the expected inputs of a workflow node, this release is
considered a minor release.

* FIX: Derive field from SyN displacements using EPI affine (#421)
* FIX: Change ``os.basename`` to ``os.path.basename`` (#419)
* DOC: Add @smeisler to contributors (#420)

2.7.0 (December 18, 2023)

New feature release in the 2.7.0 series.

This release includes an updated CLI, which allows ``sdcflows`` to be
run as a BIDS App. To achieve the previous behavior of ``sdcflows-find-estimators``,
use the ``-n`` flag.

Addtional bug fixes and enhancements are included.

* FIX: Drop header before resampling image to avoid unsafe cast (#415)
* FIX: Wrangler now ignores ``part-phase`` EPI files (#407)
* ENH: Standalone CLI now estimates fieldmaps (#408)
* ENH: Add support for ASL data (#411)
* ENH: Enable rendering of the Jupyter notebooks (#409)
* MNT: Migrate to PEP517/518 packaging (#410)
* CI: bump actions/setup-python from 4 to 5 (#412)
* CI: bump conda-incubator/setup-miniconda from 2 to 3 (#406)