22.0.4

What's Changed

• ENH: Bump Docker base to latest release by @oesteban in #1022
• FIX: Major improvements to new datalad-based interface & perform within containers by @oesteban in #1024

Full Changelog: 22.0.3...22.0.4

22.0.3

What's Changed

• MAINT: Fix failing tests as python setup.py is deprecated by @oesteban in #1013
• MAINT: Update the T1w IQMs to the new reference after #997 by @oesteban in #1014
• ENH: New version of the rating widget by @oesteban in #1012
• MAINT: Several critical updates to CircleCI and Docker images by @oesteban in #1016
• MAINT: Fix statsmodels dependency, it is not optional by @oesteban in #1017
• DOC: Move readthedocs to use the config v2 file (YAML) by @oesteban in #1018
• set rat-specific defaults for FD calculations by @eilidhmacnicol in #1005
• ENH: Add a new DataladIdentityInterface by @oesteban in #1020
• remove slice-timing correction by @psadil in #1019
• FIX: SynthStrip preprocessing miscalculating new shape after reorientation by @oesteban in #1021

New Contributors

• @psadil made their first contribution in #1019

Full Changelog: 22.0.1...22.0.3

22.0.2

What's Changed

• MAINT: Fix failing tests as python setup.py is deprecated by @oesteban in #1013
• MAINT: Update the T1w IQMs to the new reference after #997 by @oesteban in #1014
• ENH: New version of the rating widget by @oesteban in #1012
• MAINT: Several critical updates to CircleCI and Docker images by @oesteban in #1016
• MAINT: Fix statsmodels dependency, it is not optional by @oesteban in #1017
• DOC: Move readthedocs to use the config v2 file (YAML) by @oesteban in #1018

Full Changelog: 22.0.1...22.0.2

22.0.1

What's Changed

• FIX: More lenient handling of skull-stripped datasets by @oesteban in #997

Full Changelog: 22.0.0...22.0.1

22.0.0

Release Notes

First official release after migrating the repository into the NiPreps' organization.
A major new feature is the rodent pipeline by Eilidh MacNicol (@eilidhmacnicol).
A second major feature is the adoption of the updated carpet plots for BOLD fMRI,
contributed by Céline Provins (@celprov).
Virtual memory allocation has been ten-fold cut down, and a complementary resource monitor instrumentation is now available with MRIQC.
This release updates the Docker image with up-to-date dependencies, updates
MRIQC's codebase to the latest NiTransforms and includes some minor bugfixes.
The code, modules and data related to the MRIQC classifier have been extracted into an
isolated package called MRIQC-learn.
Finally, this release also contains a major code style overhaul by Zvi Baratz.

The contributor/author crediting system has been adapted to the current draft of the
NiPreps Community Governance documents.

With thanks to @ZviBaratz, @nbeliy, @octomike, @benkay86, @verdurin, @leej3, @utooley,
and @jAchtzehn for their contributions.

CHANGES

• FIX: Inconsistent API in anatomical CNR computation (#995)
• FIX: Check sanity of input data before extracting IQMs (#994)
• FIX: Plot segmentations after dropping off-diagonal (#989)
• FIX: Replace all deprecated nibabel.get_data() in anatomical module (#988)
• FIX: Resource profiler was broken with config file (#981)
• FIX: preserve WM segments in rodents (#979)
• FIX: Pin jinja2 < 3.1 (#978)
• FIX: Make toml config unique, works around #912 (#960)
• FIX: Nipype multiproc plugin expects n_procs and not nprocs (#961)
• FIX: Set TR when generating carpetplots (enables time for X axis) (#971)
• FIX: template_resolution deprecation warning (#941)
• FIX: Set entity datatype in BIDSLayout queries (#942)
• FIX: T2w image of MNI template unavailable in Singularity (#940)
• FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token (#938)
• FIX: Revise building documentation at RTD after migration (#935)
• FIX: Final touch-ups in the maintenance of Docker image + CI (#928)
• FIX: Update unit tests (#927)
• FIX: Update dependencies and repair BOLD workflow accordingly (#926)
• FIX: Update dependencies and repair T1w workflow accordingly (#925)
• FIX: Set matplotlib on Agg output mode (#892)
• ENH: Deprecate --start-idx / --stop-idx (#993)
• ENH: Add SynthStrip base module (#987)
• ENH: Improve building workflow message feedback (#990)
• ENH: Add instrumentation to monitor resources (#984)
• ENH: Standalone, lightweight version of MultiProc plugin (#985)
• ENH: Revise plugin and workflow initialization (#983)
• ENH: Base generalization of the pipeline for rodents (#969)
• ENH: Update to new NiWorkflows' API, which adds the crown to the carpetplot (#968)
• ENH: Optimize PyBIDS' layout initialization (#939)
• ENH: Refactored long strings to a :mod:mriqc.messages module (#901)
• ENH: Refactored :mod:mriqc.interfaces.common module (#901)
• DOC: Improve documentation of --nprocs and --omp-nthreads (#986)
• DOC: Add sbatch file example for SLURM execution (#963)
• DOC: Various fixes to "Running mriqc" section (#897)
• MAINT: Refactor Dockerfile using new miniconda image (#974)
• MAINT: Outsource the classifier into nipreps/mriqc-learn (#973)
• MAINT: Update CONTRIBUTORS.md (#953)
• MAINT: Update contributer location (#952)
• MAINT: Updates to CONTRIBUTORS.md file
• MAINT: Revise Docker image settings & CircleCI (#937)
• MAINT: Finalize transfer to nipreps organization (#936)
• MAINT: Relicensing to Apache-2.0, for compliance with NiPreps and prior transfer to the org (#930)
• MAINT: New Docker layer caching system of other NiPreps (#929)
• MAINT: Code style overhaul (#901)
• MAINT: Update Dockerfile and catch-up with fMRIPrep's (#924)
• STY: Run black at the top of the repo (#932)

Full Changelog: 0.16.1...22.0.0

22.0.0rc1

What's Changed

• DOC: Tiny "Running mriqc" docs fix by @ZviBaratz in #897
• FIX: TCL and display error by @nbeliy in #892
• MAINT: Miscellaneous updates by @ZviBaratz in #901
• MAINT: Update Dockerfile and catch-up with fMRIPrep's by @oesteban in #924
• FIX: Update dependencies and repair T1w workflow accordingly by @oesteban in #925
• FIX: Update dependencies and repair BOLD workflow accordingly by @oesteban in #926
• FIX: Update unit tests by @oesteban in #927
• FIX: Final touch-ups in the maintenance of Docker image + CI by @oesteban in #928
• MAINT: New Docker layer caching system of other NiPreps by @oesteban in #929
• STY: Run black at the top of the repo by @oesteban in #932
• MAINT: Relicensing to Apache-2.0, for compliance with NiPreps and prior transfer to the org by @oesteban in #930
• FIX: Revise building documentation at RTD after migration by @oesteban in #935
• MAINT: Finalize transfer to nipreps organization by @oesteban in #936
• MAINT: Revise Docker image settings & CircleCI by @oesteban in #937
• FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token by @oesteban in #938
• FIX: T2w image of MNI template unavailable in Singularity by @oesteban in #940
• ENH: Optimize PyBIDS' layout initialization by @oesteban in #939
• FIX: Set entity datatype in BIDSLayout queries by @oesteban in #942
• FIX: template_resolution deprecation warning by @oesteban in #941
• MAINT: Updating contributor info per request by @justbennet in #944
• MAINT: Update affiliations by @Shotgunosine in #945
• MAINT: Add @pvelasco's ORCID by @pvelasco in #946
• MAINT: Remove @apiccirilli by @apiccirilli in #948
• MAINT: Update CONTRIBUTORS.md by @ZviBaratz in #947
• MAINT: Update contributer location by @jdkent in #952
• MAINT: Update CONTRIBUTORS.md by @leej3 in #953
• DOC: Add sbatch file example for SLURM execution by @celprov in #963
• ENH: Update to new niworkflows' API, which adds the crown to the carpetplot by @celprov in #968
• FIX: Set TR when generating carpetplots (enables time for X axis) by @oesteban in #971
• FIX: Nipype multiproc plugin expects n_procs and not nprocs by @octomike in #961
• MAINT: Outsource the classifier into nipreps/mriqc-learn by @oesteban in #973
• FIX: Make toml config unique, works around #912 by @octomike in #960
• MAINT: Refactor Dockerfile using new miniconda image by @oesteban in #974

New Contributors

• @ZviBaratz made their first contribution in #897
• @nbeliy made their first contribution in #892
• @leej3 made their first contribution in #953
• @celprov made their first contribution in #963

Full Changelog: 0.16.1...22.0.0rc1

21.0.0rc2

First official release after migrating the repository into the *NiPreps*' organization.
This release updates the Docker image with up-to-date dependencies, updates
*MRIQC*'s codebase to the latest *NiTransforms* and includes some minor bugfixes.
Finally, this release also contains a major code style overhaul by Zvi Baratz.
With thanks to @ZviBaratz, @nbeliy, @octomike, @benkay86, @verdurin, and @utooley for their contributions.

  * FIX: ``template_resolution`` deprecation warning (#941)
  * FIX: Set entity ``datatype`` in ``BIDSLayout`` queries (#942)
  * FIX: T2w image of MNI template unavailable in Singularity (#940)
  * FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token (#938)
  * FIX: Revise building documentation at RTD after migration (#935)
  * FIX: Final touch-ups in the maintenance of Docker image + CI (#928)
  * FIX: Update unit tests (#927)
  * FIX: Update dependencies and repair BOLD workflow accordingly (#926)
  * FIX: Update dependencies and repair T1w workflow accordingly (#925)
  * FIX: Set ``matplotlib`` on ``Agg`` output mode (#892)
  * ENH: Optimize *PyBIDS*' layout initialization (#939)
  * ENH: Refactored long strings to a :mod:`mriqc.messages` module (#901)
  * ENH: Refactored :mod:`mriqc.interfaces.common` module (#901)
  * DOC: Various fixes to "Running mriqc" section (#897)
  * MAINT: Updates to ``CONTRIBUTORS.md`` file
  * MAINT: Revise Docker image settings & CircleCI (#937)
  * MAINT: Finalize transfer to ``nipreps`` organization (#936)
  * MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org (#930)
  * MAINT: New Docker layer caching system of other *NiPreps* (#929)
  * MAINT: Code style overhaul (#901)
  * MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s (#924)
  * STY: Run ``black`` at the top of the repo (#932)

21.0.0rc1

First official release after migrating the repository into the *NiPreps*' organization.
This release updates the Docker image with up-to-date dependencies, updates *MRIQC*'s codebase to the latest *NiTransforms* and includes some minor bugfixes.
Finally, this release also contains a major code style overhaul by Zvi Baratz (@zvibaratz).
With thanks to Zvi Baratz, Nikita Beliy, Michael (@octomike), Benjamin
Kay, Adam Huffman, and Ursula Tooley for their contributions.

  * FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token (#938)
  * FIX: Revise building documentation at RTD after migration (#935)
  * FIX: Final touch-ups in the maintenance of Docker image + CI (#928)
  * FIX: Update unit tests (#927)
  * FIX: Update dependencies and repair BOLD workflow accordingly (#926)
  * FIX: Update dependencies and repair T1w workflow accordingly (#925)
  * FIX: Set ``matplotlib`` on ``Agg`` output mode (#892)
  * ENH: Refactored long strings to a :mod:`mriqc.messages` module (#901)
  * ENH: Refactored :mod:`mriqc.interfaces.common` module (#901)
  * DOC: Various fixes to "Running mriqc" section (#897)
  * MAINT: Revise Docker image settings & CircleCI (#937)
  * MAINT: Finalize transfer to ``nipreps`` organization (#936)
  * MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org (#930)
  * MAINT: New Docker layer caching system of other *NiPreps* (#929)
  * MAINT: Code style overhaul (#901)
  * MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s (#924)
  * STY: Run ``black`` at the top of the repo (#932)

21.0.0rc0

First official release after migrating the repository into the *NiPreps*' organization.
This release updates the Docker image with up-to-date dependencies, updates
*MRIQC*'s codebase to the latest *NiTransforms* and includes some minor bugfixes.
Finally, this release also contains a major code style overhaul by Zvi Baratz (@zvibaratz).
With thanks to Zvi Baratz, Nikita Beliy, Michael (@octomike), Benjamin Kay, Adam Huffman,
and Ursula Tooley for their contributions.

  * FIX: Revise building documentation at RTD after migration (#935)
  * FIX: Final touch-ups in the maintenance of Docker image + CI (#928)
  * FIX: Update unit tests (#927)
  * FIX: Update dependencies and repair BOLD workflow accordingly (#926)
  * FIX: Update dependencies and repair T1w workflow accordingly (#925)
  * FIX: Set ``matplotlib`` on ``Agg`` output mode (#892)
  * ENH: Refactored long strings to a :mod:`mriqc.messages` module (#901)
  * ENH: Refactored :mod:`mriqc.interfaces.common` module (#901)
  * DOC: Various fixes to "Running mriqc" section (#897)
  * MAINT: Revise Docker image settings & CircleCI (#937)
  * MAINT: Finalize transfer to ``nipreps`` organization (#936)
  * MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org (#930)
  * MAINT: New Docker layer caching system of other *NiPreps* (#929)
  * MAINT: Code style overhaul (#901)
  * MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s (#924)
  * STY: Run ``black`` at the top of the repo (#932)

0.16.1

Release Notes

Bug-fix release in 0.16.x series.

This PR improves BIDS Derivatives compliance, fixes an issue with reading datasets with subjects of the form sub-sXYZ, and improves compatibility with more recent matplotlib.

CHANGES

• FIX: Participant labels starting with [sub] cannot be used (#890)
• FIX: Change deprecated normed to density in parameters to hist() (#888)
• ENH: Write derivatives metadata (#885)
• ENH: Add --pdb option to make debugging easier (#884)