nipreps/mriqc 22.0.0

on GitHub

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