1.5.5

Release Notes

Bug-fix release in the 1.5.x series.

CHANGES

• FIX: Correctly select volumetric spaces for carpetplot (#1932) @effigies
• FIX: Constrain setuptools for Python 2.7 installs of fmriprep-docker (#1933) @effigies

1.5.4

Release Notes

Bug-fix release in the 1.5.x series.

CHANGES

• FIX: Integrate fix for nipreps/sdcflows#77 (pinning niworkflows-1.0.3, sdcflows-1.0.3) @oesteban

1.5.3

fMRIPrep 1.5.3 (December 12, 2019)

The last bug fix release of the 1.5.x series.

• FIX: Do not run STC if SliceTiming metadata is set but empty (#1854) @oesteban
• FIX: Link to EPINorm issue in README (#1903) @adelavega
• FIX: Respect --dummy-scans 0 (#1908) @jdkent
• ENH: Upgrade SDCFlows to new API (1.0.0) (#1886) @oesteban
• ENH: Add --fs-subjects-dir flag (#1901) @effigies
• DOC: Improving accessibility of confounds description (#1877) @kfinc
• MAINT: Ensure data is packaged in sdist (#1902) @effigies
• MAINT: Remove deprecated command-line arguments (#1909) @mgxd

1.5.3rc2

pin(sdcflows): update to new bugfix release [skip ci]

1.5.3rc1

rel(1.5.3rc1): Update CHANGES [skip ci]

1.5.2

Release Notes

Bug-fix release in the 1.5.x series.

CHANGES

• FIX: Ensure data type of masked image matches T1.mgz (nipreps/niworkflows#430) @effigies

1.5.1

Release Notes

After an arduous walk through release-candidates, release 1.5.1 includes a new release of
Nipype which addresses the problems related to results files many users have been experiencing.

With thanks to Marc Bue, Alejandro De La Vega, Tailor Salo, Asier Erramuzpe and Soichi Hayashi.

CHANGES

• FIX: Treat missing field maps as empty list instead of None (#1820) @tsalo
• FIX: Raise error if work_dir is a child of bids_dir (#1860) @adelavega
• FIX: Change ICA-AROMA filenames to fit current naming scheme (#1861) @jdkent
• FIX: Update code-server in the Dockerfile_devel (#1852) @erramuzpe
• FIX: Do not generate desc-smoothAROMAnonaggr_bold conversions on standard spaces (#1838) @oesteban
• FIX: Skip plotting step of ICA-AROMA (#1834) @oesteban
• FIX: Error during version check trying to access read-only file systems (#1830) @oesteban
• FIX: Bad results files loads; PIN: nipy/nipype master (#1806) @effigies
• FIX: Adding comma to outputnode in init_func_preproc_wf (#1795) @marcbue
• FIX: Ignore sourcedata and derivatives when fetching data (#1788) @effigies
• ENH: Added skip_citation_process flag to skip processing citation.md (#1876) @soichih
• ENH: Restore space-MNI152NLin6Asym for AROMA denoised outputs (#1839) @oesteban
• ENH: Confounds metadata (#1708) @rciric
• DOC: Remove OpenNeuro badge (#1862) @adelavega
• DOC: Improve documentation about TemplateFlow and Containers (#1802) @oesteban
• DOC: Add VERSION argument to docker build instructions (#1797) @effigies
• DOC: Revise docstrings of workflows for correct parsing with napoleon #1882 (@oesteban)
• CI: Use recent Python image to build packages (#1790) @effigies
• MAINT: Update to the new API of sMRIPrep (#1879) @adelavega
• MAINT: Update CONTRIBUTING.md inspired by dMRIPrep's (#1853) @oesteban
• MAINT: Enable circleci-artifacts-redirector (#1857) @effigies
• MAINT: Cleaning up dependencies (#1832) @oesteban
• MAINT: Pin Python 3.7.4 in CircleCI's build_docs (#1836) @oesteban
• MAINT: Purge Cython and depend on SDCflows (#1792) @effigies
• MAINT: Container images - cleanup $HOME in docker build (#1768) @oesteban

1.5.1rc2

Release Notes

A second release candidate on the way to 1.5.1, with minor bugfixes and improvements.

CHANGES

• ENH: Restore space-MNI152NLin6Asym for AROMA denoised outputs (#1839) @oesteban
• FIX: Do not generate desc-smoothAROMAnonaggr_bold conversions on standard spaces (#1838) @oesteban
• MAINT: Cleaning up dependencies (#1832) @oesteban
• FIX: Skip plotting step of ICA-AROMA (#1834) @oesteban
• FIX: Error during version check trying to access read-only file systems (#1830) @oesteban
• MAINT: Pin Python 3.7.4 in circle's build_docs (#1836) @oesteban

1.5.1rc1

Release Notes

Bugfixes and maintenance on the way to 1.5.1. in particular, the later problems with nipype 1.2.2 should improve with the pinning of 1.3.0rc1. With thanks to @marcbue

CHANGES

• MAINT: Purge Cython and depend on SDCflows (#1792) @effigies
• DOC: Improve documentation about TemplateFlow and Containers (#1802) @oesteban
• FIX: Bad results files loads; PIN: nipy/nipype master (#1806) @effigies
• FIX: Adding comma to outputnode in init_func_preproc_wf (#1795) @marcbue
• DOC: Add VERSION argument to docker build instructions (#1797) @effigies
• FIX: Ignore sourcedata and derivatives when fetching data (#1788) @effigies
• CI: Use recent Python image to build packages (#1790) @effigies
• ENH: Confounds metadata (#1708) @rciric
• MAINT: Container images - cleanup $HOME in docker build (#1768) @oesteban

1.5.0

Release Notes

Two hallmark changes conducive to a new minor release line have been included in version 1.5.0: the upgrade of PyBIDS to the 0.9 series and the split of SDCflows off from fMRIPrep codebase. PyBIDS 0.9.x has a better handling of the indexed dataset that will permit some optimizations to fMRIPrep's memory fingerprint. SDCflows now are found at poldracklab/sdcflows, and have been split to allow a more granular and thorough testing in collaboration with M. Cieslak, A. Adebimpe, and T. Satterthwaite.
Some other bugfixes, improvements to the documentation and minor features are also shipped with the new release. With thanks to Ursula Tooley, Sebastian Urchs and Gabriel A. Devenyi for contributions.

CHANGES

• FIX: Minor improvements for templateflow installation in Docker images (#1764) @oesteban
• FIX: Passing surface template keywords into carpetplot workflow (#1755) @oesteban
• FIX: Postpone pandoc conversion of boilerplate after workflow has fully run (#1710) @oesteban
• FIX: Use MNI152NLin2009cAsym for SDC if no templates are specified (#1703) @effigies
• FIX: Correct BOLD-T1w registration description if DoF != 9 (#1701) @effigies
• ENH: Set up code-server docker recipe for interactive development (#1730) @jdkent
• ENH: Make fmriprep print defaults for arguments with help (#1735) @gdevenyi
• ENH: Add check for updates and check whether version has been flagged. (#1715) @oesteban
• ENH: Add TaskName metadata to BOLD outputs (#1714) @effigies
• REF: Separate SDCflows from fMRIPrep (#1670) @oesteban
• DOC: Adding fmriprep benchmark info to FAQs (#1759) @surchs
• DOC: Update .zenodo.json (#1732) @utooley
• DOC: Add link to documentation in help of --output-spaces argument (#1722) @oesteban
• DOC: adding recon-all issue to faq (#1622) @franklin-feingold
• DOC: Add copyright waiver to boilerplate and reviewer note to docs (#1691) @effigies
• MAINT: niworkflows and nipype to use latest N4BiasFieldCorrection (#1752) @oesteban
• MAINT: Bump pybids and nipype dependencies (#1744) @effigies
• MAINT: Move regression tests of EPI masks over to Niworkflows (#1716) @oesteban
• MAINT: Remove old extensions entity selector for PyBIDS queries (#1707) @oesteban
• MAINT: Use PyBIDS 0.9.x via niworkflows/smriprep PRs (#1695) @effigies