Warning: This document is for an old version of smriprep. The main version is master.

What’s new?

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)

0.5.2 (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

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 poldracklab/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 poldracklab/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