0.19.1

Release Notes

Bug-fix release in the 0.19.x series.

Fixed a package metadata error.

0.19.0

Release Notes

New feature release in the 0.19.x series.

This release enables per-session processing and more flexible surface resampling.

Changelog

• FIX: Collate pre-computed transforms correctly (#487)
• ENH: Resample surfaces to any space/density using Connectome Workbench. (#473)
• ENH: Generate cortex mask in during fit stage (#482)
• ENH: Use output surfaces in internal nodes, ensuring greater consistency (#483)
• ENH: Enable per-session processing (#480)
• DOC: Fix typo in citation boilerplate (sMRIPprep → sMRIPrep) (#489)
• STY: ISC rules do not conflict with the formatter any more (#484)

0.18.0

Release notes

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.

Changes

• 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

Release notes

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.

Changes

• 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)

Full Changelog: 0.16.1...0.17.0

0.16.1

Release Notes

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

Changelog

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

0.16.0

Release Notes

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.

Changelog

• 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

Release Notes

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.

Changelog

• 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

Release notes

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.

Changes

• 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)

Full Changelog: 0.13.2...0.14.0

0.13.2

Release notes

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.

Changes

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

Full Changelog: 0.13.1...0.13.2

0.13.1

Release notes

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.

Changes

• FIX: T1w_preproc -> t1w_preproc (#399)

Full Changelog: 0.13.0...0.13.1