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

1.5.0 RC2

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.

CHANGES

• 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: 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: 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: 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

1.5.0rc1

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.

CHANGES

• ENH: Add TaskName metadata to BOLD outputs (#1714) @effigies
• REF: Separate SDCflows from fMRIPrep (#1670) @oesteban
• MAINT: Remove old extensions entity selector for PyBIDS queries (#1707) @oesteban
• FIX: Postpone pandoc conversion of boilerplate after workflow has fully run (#1710) @oesteban
• DOC: adding recon-all issue to faq (#1622) @franklin-feingold
• FIX: Use MNI152NLin2009cAsym for SDC if no templates are specified (#1703) @effigies
• FIX: Correct BOLD-T1w registration description if DoF != 9 (#1701) @effigies
• MAINT: Use PyBIDS 0.9.x via niworkflows/smriprep PRs (#1695) @effigies
• DOC: Add copyright waiver to boilerplate and reviewer note to docs (#1691) @effigies

1.4.1

Release Notes

As of 1.4.1, the new infant and pediatric templates added to TemplateFlow are available to
brain extraction and spatial normalization.
Containers do not set the TEMPLATEFLOW_HOME environment variable anymore, allowing
increased flexibility when running them (especially Singularity, for which the filesystem
is generally set read-only).
Additionally, BOLD files in native space can be generated and a minor bug related to the
handling of FreeSurfer outputs have been included.

CHANGES

• ENH: Show informative warning for phase1/2 type of fieldmaps (#1689) @oesteban
• DOC: Add WHT to Zenodo (#1683) @wiheto
• FIX: Finalizing support for new templates and their command line modifiers (#1671) @oesteban
• FIX: Do not set TEMPLATEFLOW_HOME (#1669) @oesteban
• ENH: Allow template modifiers (a la --output-spaces) in skull-stripping (#1666) @oesteban
• ENH: Write outputs in native-BOLD space (#1646) @oesteban
• FIX: FreeSurfer failed without adding some fs* to --output-spaces (#1643) @oesteban

1.4.1rc5

rel(1.4.1): Update CHANGES [skip ci]

1.4.1rc4

Merge pull request #1671 from oesteban/anat/improved-several-templates

FIX: Finalizing support for new templates and their command line modifiers