What’s new?

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)

0.12.1 (June 15, 2023)

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.

FIX: Pass sphere_reg_fsLR to ds_reg_fsLR (#350)

0.12.0 (June 05, 2023)

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.

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

0.11.1 (March 23, 2023)

Bug-fix release in the 0.11.x series.

This release changes the default name of a workflow. This change modifies the workflow structure superficially, but in such a way that reusing a working directory should present no possibility of error.

RF: Reflect function name on nipype workflow (#328)
DOC: Update boilerplate generation with TemplateFlow reference (#329)

0.11.0 (March 10, 2023)

New feature release in the 0.11.x series.

This series supports fMRIPrep 23.0.x.

This release drops support for Python 3.7.

ENH: Enable resampling morphometrics to fsLR CIFTI-2 files (#325)
ENH: Add cortical ribbon workflow (#322)
ENH: Merge T2w images and coregister to T1w template (#319)
MAINT: Rotate CircleCI secrets and setup up org-level context (#315)
CI: Update build to match fMRIPrep (#323)

0.10.0 (November 30, 2022)

New feature release in the 0.10.x series.

This series supports fMRIPrep 22.1.x and Nibabies 22.2.x.

This will be the last series to support Python 3.7.

FIX: Expand surfaces pattern to allow morphometrics (#312)
ENH: Bind FreeSurfer subjects directory (#311)
ENH: Output thickness, curvature, and sulcal depth files (#305)
WRAPPER: Update patch location, use –patch syntax (#309)
CI: Fix expected ds054 outputs (#310)
CI: Set max Python version to 3.10 (#308)
CI: Simplify actions to build once, test many (#304)
CI: Update CircleCI docker orb (#302)

0.9.2 (July 20, 2022)

Bug-fix release in the 0.9.x series.

With thanks to Eric Feczko for tracking down a fiddly bug.

FIX: Use mris_convert –to-scanner, and update normalization step (#295)

0.9.1 (July 14, 2022)

Bug-fix release in the 0.9.x series.

This release contains patches for supporting FreeSurfer 7.2.

FIX: Disable -T2pial and -FLAIRpial at -autorecon1 stage (#291)

FIX: Re-add missing getfullpath FreeSurfer binary (#290)

FIX: Re-add fsr-checkxopts to Docker image (#287)

0.9.0 (May 26, 2022)

A new minor release incorporating support for FreeSurfer 7.2.

DOC: Fix build (#283)

DOCKER: Bundle FreeSurfer 7.2 (#281)

FIX: Override nipype handling of recon-all hemi input (#282)

0.8.3 (February 08, 2022)

Patch release in the 0.8.x series. This allows compatibility with the next minor release of niworkflows.

DOC: Update scipy intersphinx url (#276)

MAINT: Allow compatibility with new niworkflows minor (#277)

0.8.2 (December 13, 2021)

Patch release in the 0.8.x series.

This release includes some minor formatting fixes to the generated workflow boilerplate. Additionally, the Docker image environment was updated.

DOCKER: Update Dockerfile to match fMRIPrep, using FSL 6 (#274)

FIX: Generated boilerplate formatting (#275)

0.8.1 (October 08, 2021)

Bug-fix release in the 0.8.x series.

All releases since 0.5.3 have incorrectly resampled the (aparc+)aseg segmentations with trilinear interpolation, rather than nearest-neighbor. This fix has also been applied in 0.7.2, to provide a fix in the fMRIPrep LTS series.

FIX: Resample aseg with nearest-neighbor interpolation (#268)

0.8.0 (September 1, 2021)

A new minor release incorporating small iterations and improvements on NiWorkflows, and including some bug-fixes/enhancements.

DOC: Ensure copyright notice is found in all Python files (#248)
FIX: Revert to FAST for tissue probability segmentations (#263)
FIX: Sturdier version check of sMRIPrep-wrapper package (#245)
FIX: Do not use deprecated --filter pandoc-citeproc generating boilerplate (e72eea5)
FIX: Mask T1w images before transforming to template (#237)
FIX: Account for label entity when querying brain mask (#257)
MAINT: Run pytest on GitHub Actions (#262)
MAINT: Mount TemplateFlow’s home directory in CircleCI tests (#246)
MAINT: Run black at the top level of the repo (#241)
MAINT: Update to new API of NiWorkflows (#239)
MAINT: Refactor Dockerfile and move tests from TravisCI to GHA (#240)
MAINT: Use separate fallback cache for maint/0.7.x (#250)
MAINT: CircleCI housekeeping (#258) (#259)

0.7.2 (October 07, 2021)

Bug-fix release in the 0.7.x series.

All releases since 0.5.3 have incorrectly resampled the (aparc+)aseg segmentations with trilinear interpolation, rather than nearest-neighbor. This also reverts to using FAST for tissue probability maps, as the calculations from FreeSurfer’s segmentation are less straightforward.

FIX: Resample aseg with nearest-neighbor interpolation (#268)

FIX: Revert to FAST for tissue probability maps (#264)

CI: Use separate fallback cache for maint/0.7.x (#250)

0.7.1 (November 18, 2020)

Bug-fix release in the 0.7.x series.

All releases since 0.4.0 have incorrectly labelled T1w images normalized to a template space as SkullStripped in the corresponding JSON sidecar files. This affects 0.4.x through 0.4.2, 0.5.x through 0.5.3, 0.6.x through 0.6.2, and 0.7.0. Prior to 0.4.0, the images were actually skull-stripped, and the metadata labels were not incorrect.

For backwards compatibility reasons, any future releases of these series will have SkullStripped set to False. In 0.8 and above, the images will be skull-stripped and the metadata set back to True.

CI: CircleCI housekeeping (#234, #235)

0.7.0 (September 27, 2020)

Minor release in preparation for fMRIPrep 20.2.x LTS series. Includes minor features and bug-fixes over the previous 0.6 series.

FIX: Pin NiWorkflows 1.3.1 including bugfix for INU-correction failures (nipreps/niworkflows#567)
FIX: Generate anatomical conversions with full spec from --output-spaces (#219)
FIX: Ordering of probseg maps with anatomical fast-track (#214)
FIX: Progress partial volume maps instead of posteriors (FSL FAST) (#213)
ENH: Retain session info when multi-session data are not averaged (#225)
ENH: Update derivatives description, .bidsignore for derivatives (#220)
ENH: Add --no-tty option to Docker wrapper (#216)
ENH: Add function to handle stale IsRunning files (#207)
MAINT: Upgrade ANTs to 2.3.4 in Dockerfile (365673b)
MAINT: Make workflows keyword-only (PEP 3102) (#208)

0.6.2 (June 9, 2020)

Bug-fix release addressing minor problems related to FreeSurfer handling.

FIX: Adapt to the new FS canary interface (backwards compatible) (#205)
FIX: Use t1w2fsnative_xfm to resample segmentations (#201)

0.6.1 (May 27, 2020)

Hotfix release to address an issue recently encountered in fMRIPrep 20.1.0rc3.

FIX: MultiLabel interpolations should not use float=True (#196)

0.6.0 (May 22, 2020)

Minor release in preparation for fMRIPrep 20.1.x series. Features the new implementation of derivatives writers in NiWorkflows, and additional flexibility to use previously computed results (in particular, skull-stripped brains, and the new fast-track that allows skipping the anatomical workflow in full, if all the expected derivatives are provided). Most of the the bug-fixes correspond to amendments over these newly added features.

FIX: Convert LTA to ITK with nitransforms (#188)
FIX: Dismiss session entity on most of anatomical derivatives (#193)
FIX: Revise tissue probability maps connections and order (#190)
FIX: Make TPMs label ordering in io_spec.json consistent with workflow (#179)
FIX: Correct the dseg labeling from FSL FAST earlier (#177)
FIX: Ensure bias_corrected is single file, not list (#174)
ENH: Use new DerivativesDataSink from NiWorkflows 1.2.0 (#183)
ENH: Use FreeSurfer’s canary to exit fast and with a clear message when the license is missing (#182)
ENH: Execute FSL FAST only with --fs-no-reconall (#180)
ENH: Enable anatomical fast track reusing existing derivatives (#107)
ENH: Add option to skip brain extraction (#167)
MAINT: Remove unused nwf interfaces (#187)
MAINT: Pin troublesome sphinx (#175)
MAINT: Update dependencies to be inline with fMRIPrep-20.1.x (#173)

0.5.x Series

0.5.3 (June 7, 2020)

Bug-fix release in the 0.5.x series.

This release fixes a bug where pre-run FreeSurfer that was not in alignment with the T1w template generated by fMRIPrep could result in misaligned segmentation and mask derivatives.

The bug is most likely to occur with pre-run FreeSurfer where multiple T1w images are found. It is easily evident in the first figure in the anatomical section of the reports, and will show heavily misaligned brain mask.

FIX: Use t1w2fsnative_xfm to resample segmentations (#201) @effigies

0.5.2 (February 14, 2020)

Minor tweaks in preparation for fMRIPrep 20.0.0 release.

ENH: Enable users to pass JSON filters to select subsets of data (#143) @bpinsard
MAINT: Add ignore W503 in setup.cfg (#165) @oesteban

0.5.1 (February 7, 2020)

A hotfix release updating dependencies

PIN: Nibabel 3.0.1 and niworkflows 1.1.6 (#166) @mgxd

0.5.0 (February 6, 2020)

A new minor release with a focus on improving internal handling and representations of spatial references.

RF: Update Spaces objects (#164) @mgxd
ENH: Fix template keys output in normalization workflow, when cohort present (#163) @oesteban
ENH: Integrate new infrastructure in NiWorkflows to handle spatial references (#159) @mgxd
FIX: Improvements to the CircleCI workflow (#162) @oesteban
CI: Update coverage (#156) @effigies

Pre- 0.5.x Series

0.4.2 (January 22, 2020)

Bugfix release in the 0.4.x series.

FIX: Calculate FoV with shape and zooms (#161) @effigies
FIX: Package version incorrect within Docker image (#155) @oesteban
ENH: Add smriprep.__main__ to allow python -m smriprep (#158) @effigies
MAINT: Revise CircleCI to optimize TemplateFlow and caching (#157) @oesteban

0.4.1 (Decemeber 12, 2019)

Bugfix release to address some fMRIPrep issues.

FIX: Use T2/FLAIR refinement at cortribbon stage (#148) @effigies
FIX: empty specs for legacy/nonstd spaces (#146) @mgxd
DOC: Refactor of documentation (#144) @oesteban

0.4.0 (November 26, 2019)

A new 0.4.x series with a number of new features and bugfixes.

FIX: Allow setting nonstandard spaces for parser (#141) @oesteban
FIX: Normalization workflow API - provide bare template names (#139) @oesteban
FIX: Build smriprep-docker like fmriprep-docker (#138) @oesteban
FIX: Check template identifiers are valid early (#135) @oesteban
FIX: Re-organize FreeSurfer stages to avoid duplication and races (#117) @effigies
FIX: Revise naming of transforms when several T1w images are averaged (#106) @oesteban
FIX: Allow setting nonstandard spaces for parser (#141) @oesteban
ENH: Add --fs-subjects-dir flag (#114) @effigies
ENH: Add smriprep-docker wrapper (#118) @effigies
ENH: Add a README.rst (#103) @oesteban
ENH: Decoupling anatomical reports (#112) @oesteban
ENH: Reduce friction when iterating over target templates (#111) @oesteban
ENH: Write out the fsnative-to-T1w transform (#113) @oesteban
DOC: Minimal refactor preparing release (#140) @oesteban
DOC: Revise numpy docstrings so they are correctly rendered (#134) @oesteban
DOC: Deploy docs to gh-pages from CircleCI - with versioning (#65) @rwblair
CI: Optimize CircleCI using a local docker registry instead docker save/load (#136) @oesteban
CI: Run pytests on Python 3.7 for now (#133) @effigies
CI: Fix packaging test (#115) @effigies
CI: Test packaging and update deploy_pypi step (#119) @effigies
MAINT: Fine-tune versioning extension of sphinx (#121) @oesteban
MAINT: Refactoring inputs/outputs names and some stylistic changes (#108) @oesteban
MAINT: Resolve issues with working directory of ds005 on CircleCI (#110) @oesteban
PIN: niworkflows ~= 1.0.0rc1

0.3.2 (September 9, 2019)

Bugfix patch-release

FIX: Render INU-corrected T1w in Segmentation reportlet (#102) @oesteban

0.3.1 (July 21, 2019)

Minor release to update pinnings of niworkflows and TemplateFlow client.

PIN: niworkflows-0.10.1 and templateflow-0.4.1
CI: Fix PyPI deployment (#99) @effigies

0.3.0 (July 12, 2019)

Minor release to allow dependent tools to upgrade to PyBIDS 0.9 series (minimum 0.9.2). We’ve also moved to a setup.cfg-based setup to standardize configuration.

MAINT: Move to setup.cfg + pyproject.toml (#98) @effigies
MAINT: Use PyBIDS 0.9.x via niworkflows PR (#94) @effigies

0.2.4 (July 9, 2019)

Several minor improvements on TemplateFlow integration.

ENH: Use proper resolution in anatomical outputs (#92) @oesteban
ENH: Indicate what templates were not found in TemplateFlow (#91) @oesteban
ENH: Pass template specs on to registration workflow (#90) @oesteban

0.2.3 (June 5, 2019)

Enable CLI to set pediatric and infant templates for skull-stripping.

ENH: Allow template modifiers (a la --output-spaces) in skull-stripping (#89) @oesteban

0.2.2 (June 5, 2019)

Enable latest templates added to TemplateFlow.

PIN: templateflow-0.3.0, which includes infant/pediatric templates (#88) @oesteban

0.2.1 (May 6, 2019)

Hotfix release improving the reliability of the brain extraction workflow.

FIX: Keep header consistency along anatomical workflow (#83) @oesteban

0.2.0 (May 3, 2019)

This new release of sMRIPrep adds the possibility of specifying several spatial normalization targets via the --output-spaces option drafted in nipreps/fmriprep#1588.

FIX: Resolve behavior when deprecated --template is given (#77) @oesteban
FIX: Solved problems in report generation (#76) @oesteban
ENH: Force compression of derivative NIfTI volumes (#80) @effigies
ENH: Pull list of spatial normalization templates from TemplateFlow (#68) @oesteban
ENH: CLI uses pathlib.Path when possible (#73) @oesteban
ENH: Create a spatial normalization workflow (#72) @oesteban
ENH: Several improvements over the new spatial normalization workflow (#74) @oesteban
ENH: Support for multiple --output-spaces (#75) @oesteban
DOC/STY: Fix documentation build, simplify (non)parametric output nodes (#79) @oesteban

0.1.1 (March 22, 2019)

ENH: Pure Nipype brain extraction workflow (#57) @oesteban
ENH: Write metadata for anatomical outputs (#62) @oesteban

0.1.0 (March 05, 2019)

PIN: Niworkflows 0.8 and TemplateFlow 0.1 (#56) @oesteban

0.0.5 (February 06, 2019)

MAINT: Update to keep up with nipreps/niworkflows#299 (#51) @oesteban

0.0.4 (January 25, 2019)

ENH: Allow templates other than MNI152NLin2009cAsym (#47) @oesteban
DOC: Fix workflow hierarchy within docstrings so that fMRIPrep docs build (0110ab2).

0.0.3 (January 18, 2019)

FIX: Add -cw256 flag for images with FoV > 256 voxels (#36) @oesteban
ENH: Integrate TemplateFlow to handle templates (#45) @oesteban

0.0.2 (January 8, 2019)

First functional version after forking from fMRIPrep