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

0.13.0

Release notes

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.

Changes

• 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)

New Contributors

• @DimitriPapadopoulos made their first contribution in #347
• @psadil made their first contribution in #357
• @dependabot made their first contribution in #391

Full Changelog: 0.12.2...0.13.0

0.12.2

Release Notes

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.

What's Changed

• DOCKER: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image by @psadil in #357

Full Changelog: 0.12.1...0.12.2

0.12.1

Release Notes

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.

What's Changed

• FIX: Pass sphere_reg_fsLR to ds_reg_fsLR by @effigies in #350

Full Changelog: 0.12.0...0.12.1

0.12.0

Release Notes

New feature release in the 0.12.x series.

This release adds ANTs DenoiseImage to T1w and T2w preprocessing, improving signal-to-noise ratio. Surface processing now produces a registration sphere to permit directly resampling data from T1w space to fsLR.

What's Changed

• FIX: Query templateflow files to see if resolution is available by @mgxd in #336
• ENH: Use ANTs DenoiseImage before conforming anatomical images by @effigies in #337
• ENH: Project fsLR mesh onto native sphere to enable single-shot resampling into fsLR by @effigies in #339
• DOC: Add security fix to vendored jquery by @mgxd in #332
• MNT: Loosen niworkflow restriction by @mgxd in #335
• CI: Prioritize tags on release by @mgxd in #331
• CI: Fix codecov in CircleCI, remove Travis config by @effigies in #333
• MNT: Add sloppy argument to workflows, distinguish from debug by @mgxd in #344

Full Changelog: 0.11.1...0.12.0