2.13.2

Release Notes

Patch release in the 2.13.x series.

This includes a fix for cases where a scan contributes to multiple B0FieldIdentifiers.

Changelog

• FIX: Fixes conditions of overlapping B0FieldIdentifier, resulting in no estimators (#497)

2.13.1

Release Notes

Patch release in the 2.13.x series.

This includes a fix to init_fmap_preproc_wf node naming.

Changes

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

2.13.0

Release Notes

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.

Changes

• 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

Release Notes

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

Changes

• 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

Release notes

Feature release in the 2.11.x series.

This release supports numpy 2 and Python 3.13.

Changes

• 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)

New Contributors

• @psadil made their first contribution in #463

Full Changelog: 2.10.0...2.11.0

2.10.0

Release Notes

Feature release in the 2.10.x series.

The main change is a bugfix when fitting multi-level B-Splines to some noisy fieldmaps. While theoretically nice, the multi-level fitting does not really bring anything immediately as we are not generally inverting the distortion. In this release, the default fitting has been changed 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.

What's Changed

• FIX: Building Docker image on ARM64 devices by @mathdugre in #449
• DOC: ValueError in notebook output by @mathdugre in #450
• ENH: Improve plots in Jupyter notebook by @oesteban in #452
• FIX: Revision of the B-Spline fitting code by @oesteban in #453

New Contributors

• @mathdugre made their first contribution in #449

Full Changelog: 2.9.0...2.10.0

2.9.0

Release notes

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.

Changes

• FIX: Update suffix only when finding related fieldmap files (#436)
• 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)

New Contributors

• @marcelzwiers made their first contribution in #436

Full Changelog: 2.8.1...2.9.0

2.8.1

Release notes

Bug-fix release in the 2.8.x series.

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

Changes

• 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)

Full Changelog: 2.8.0...2.8.1

2.8.0

Release notes

New feature release in the 2.8.x 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.

Changes

• 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)

New Contributors

• @smeisler made their first contribution in #419

Full Changelog: 2.7.0...2.8.0

2.7.0

Release notes

New feature release in the 2.7.x 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.

Changes

• 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)

New Contributors

• @tsalo made their first contribution in #411

Full Changelog: 2.6.0...2.7.0