Tags: yarikoptic/mriqc
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22.0.6 Release Notes ------------- A hotfix release partially rolling-back the previous fix nipreps#1025. Thanks everyone for your patience with the excessively rushed release of 22.0.5. CHANGES ------- * FIX: Better fix to the multi-argument ``--participant-label`` issue (nipreps#1026)
22.0.5 Release Notes ------------- A hotfix release addressing a problem with the argument parser. CHANGES ------- * FIX: Multiple valued ``--participant-label`` wrongly parsed (nipreps#1025)
22.0.4 Release Notes ------------- A hotfix release to ensure smooth operation of datalad within Docker. CHANGES ------- * FIX: Major improvements to new datalad-based interface & perform within containers (nipreps#1024) * ENH: Bump Docker base to latest release (nipreps#1022)
22.0.3 Release Notes ------------- A patch release containing a bugfix to the SynthStrip preprocessing. CHANGES ------- * FIX: SynthStrip preprocessing miscalculating new shape after reorientation (nipreps#1021) * ENH: Remove slice-timing correction (nipreps#1019) * ENH: Add a new ``DataladIdentityInterface`` (nipreps#1020) * ENH: Set rat-specific defaults for FD calculations (nipreps#1005) * ENH: New version of the rating widget (nipreps#1012) * DOC: Move readthedocs to use the config v2 file (YAML) (nipreps#1018) * MAINT: Fix statsmodels dependency, it is not optional (nipreps#1017) * MAINT: Several critical updates to CircleCI and Docker images (nipreps#1016) * MAINT: Update the T1w IQMs to the new reference after nipreps#997 (nipreps#1014) * MAINT: Fix failing tests as ``python setup.py`` is deprecated (nipreps#1013)
22.0.2 What's Changed -------------- * MAINT: Fix failing tests as ``python setup.py`` is deprecated by @oesteban in nipreps#1013 * MAINT: Update the T1w IQMs to the new reference after nipreps#997 by @oesteban in nipreps#1014 * ENH: New version of the rating widget by @oesteban in nipreps#1012 * MAINT: Several critical updates to CircleCI and Docker images by @oesteban in nipreps#1016 * MAINT: Fix statsmodels dependency, it is not optional by @oesteban in nipreps#1017 * DOC: Move readthedocs to use the config v2 file (YAML) by @oesteban in nipreps#1018 **Full Changelog**: nipreps/mriqc@22.0.1...22.0.2
22.0.1 A patch release addressing a new minor bug. * FIX: More lenient handling of skull-stripped datasets (nipreps#997)
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*](https://github.com/nipreps/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 (nipreps#995) * FIX: Check sanity of input data before extracting IQMs (nipreps#994) * FIX: Plot segmentations after dropping off-diagonal (nipreps#989) * FIX: Replace all deprecated ``nibabel.get_data()`` in anatomical module (nipreps#988) * FIX: Resource profiler was broken with config file (nipreps#981) * FIX: preserve WM segments in rodents (nipreps#979) * FIX: Pin ``jinja2 < 3.1`` (nipreps#978) * FIX: Make toml config unique, works around nipreps#912 (nipreps#960) * FIX: Nipype multiproc plugin expects ``n_procs`` and not ``nprocs`` (nipreps#961) * FIX: Set TR when generating carpetplots (enables time for X axis) (nipreps#971) * FIX: ``template_resolution`` deprecation warning (nipreps#941) * FIX: Set entity ``datatype`` in ``BIDSLayout`` queries (nipreps#942) * FIX: T2w image of MNI template unavailable in Singularity (nipreps#940) * FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token (nipreps#938) * FIX: Revise building documentation at RTD after migration (nipreps#935) * FIX: Final touch-ups in the maintenance of Docker image + CI (nipreps#928) * FIX: Update unit tests (nipreps#927) * FIX: Update dependencies and repair BOLD workflow accordingly (nipreps#926) * FIX: Update dependencies and repair T1w workflow accordingly (nipreps#925) * FIX: Set ``matplotlib`` on ``Agg`` output mode (nipreps#892) * ENH: Deprecate ``--start-idx`` / ``--stop-idx`` (nipreps#993) * ENH: Add SynthStrip base module (nipreps#987) * ENH: Improve building workflow message feedback (nipreps#990) * ENH: Add instrumentation to monitor resources (nipreps#984) * ENH: Standalone, lightweight version of MultiProc plugin (nipreps#985) * ENH: Revise plugin and workflow initialization (nipreps#983) * ENH: Base generalization of the pipeline for rodents (nipreps#969) * ENH: Update to new *NiWorkflows*' API, which adds the crown to the carpetplot (nipreps#968) * ENH: Optimize *PyBIDS*' layout initialization (nipreps#939) * ENH: Refactored long strings to a :mod:`mriqc.messages` module (nipreps#901) * ENH: Refactored :mod:`mriqc.interfaces.common` module (nipreps#901) * DOC: Improve documentation of ``--nprocs`` and ``--omp-nthreads`` (nipreps#986) * DOC: Add ``sbatch`` file example for SLURM execution (nipreps#963) * DOC: Various fixes to "Running mriqc" section (nipreps#897) * MAINT: Refactor ``Dockerfile`` using new miniconda image (nipreps#974) * MAINT: Outsource the classifier into nipreps/mriqc-learn (nipreps#973) * MAINT: Update ``CONTRIBUTORS.md`` (nipreps#953) * MAINT: Update contributer location (nipreps#952) * MAINT: Updates to ``CONTRIBUTORS.md`` file * MAINT: Revise Docker image settings & CircleCI (nipreps#937) * MAINT: Finalize transfer to ``nipreps`` organization (nipreps#936) * MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org (nipreps#930) * MAINT: New Docker layer caching system of other *NiPreps* (nipreps#929) * MAINT: Code style overhaul (nipreps#901) * MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s (nipreps#924) * STY: Run ``black`` at the top of the repo (nipreps#932) **Full Changelog**: nipreps/mriqc@0.16.1...22.0.0
22.0.0rc1 * DOC: Tiny "Running mriqc" docs fix by @ZviBaratz in nipreps#897 * FIX: TCL and display error by @nbeliy in nipreps#892 * MAINT: Miscellaneous updates by @ZviBaratz in nipreps#901 * MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s by @oesteban in nipreps#924 * FIX: Update dependencies and repair T1w workflow accordingly by @oesteban in nipreps#925 * FIX: Update dependencies and repair BOLD workflow accordingly by @oesteban in nipreps#926 * FIX: Update unit tests by @oesteban in nipreps#927 * FIX: Final touch-ups in the maintenance of Docker image + CI by @oesteban in nipreps#928 * MAINT: New Docker layer caching system of other NiPreps by @oesteban in nipreps#929 * STY: Run ``black`` at the top of the repo by @oesteban in nipreps#932 * MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org by @oesteban in nipreps#930 * FIX: Revise building documentation at RTD after migration by @oesteban in nipreps#935 * MAINT: Finalize transfer to ``nipreps`` organization by @oesteban in nipreps#936 * MAINT: Revise Docker image settings & CircleCI by @oesteban in nipreps#937 * FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token by @oesteban in nipreps#938 * FIX: T2w image of MNI template unavailable in Singularity by @oesteban in nipreps#940 * ENH: Optimize *PyBIDS*' layout initialization by @oesteban in nipreps#939 * FIX: Set entity ``datatype`` in ``BIDSLayout`` queries by @oesteban in nipreps#942 * FIX: ``template_resolution`` deprecation warning by @oesteban in nipreps#941 * MAINT: Updating contributor info per request by @justbennet in nipreps#944 * MAINT: Update affiliations by @Shotgunosine in nipreps#945 * MAINT: Add @pvelasco's ORCID by @pvelasco in nipreps#946 * MAINT: Remove @apiccirilli by @apiccirilli in nipreps#948 * MAINT: Update CONTRIBUTORS.md by @ZviBaratz in nipreps#947 * MAINT: Update contributer location by @jdkent in nipreps#952 * MAINT: Update CONTRIBUTORS.md by @leej3 in nipreps#953 * DOC: Add ``sbatch`` file example for SLURM execution by @celprov in nipreps#963 * ENH: Update to new niworkflows' API, which adds the crown to the carpetplot by @celprov in nipreps#968 * FIX: Set TR when generating carpetplots (enables time for X axis) by @oesteban in nipreps#971 * FIX: Nipype multiproc plugin expects ``n_procs`` and not ``nprocs`` by @octomike in nipreps#961 * MAINT: Outsource the classifier into ``nipreps/mriqc-learn`` by @oesteban in nipreps#973 * FIX: Make toml config unique, works around nipreps#912 by @octomike in nipreps#960 * MAINT: Refactor ``Dockerfile`` using new miniconda image by @oesteban in nipreps#974 * @ZviBaratz made their first contribution in nipreps#897 * @nbeliy made their first contribution in nipreps#892 * @leej3 made their first contribution in nipreps#953 * @celprov made their first contribution in nipreps#963 **Full Changelog**: nipreps/mriqc@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 (nipreps#941) * FIX: Set entity ``datatype`` in ``BIDSLayout`` queries (nipreps#942) * FIX: T2w image of MNI template unavailable in Singularity (nipreps#940) * FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token (nipreps#938) * FIX: Revise building documentation at RTD after migration (nipreps#935) * FIX: Final touch-ups in the maintenance of Docker image + CI (nipreps#928) * FIX: Update unit tests (nipreps#927) * FIX: Update dependencies and repair BOLD workflow accordingly (nipreps#926) * FIX: Update dependencies and repair T1w workflow accordingly (nipreps#925) * FIX: Set ``matplotlib`` on ``Agg`` output mode (nipreps#892) * ENH: Optimize *PyBIDS*' layout initialization (nipreps#939) * ENH: Refactored long strings to a :mod:`mriqc.messages` module (nipreps#901) * ENH: Refactored :mod:`mriqc.interfaces.common` module (nipreps#901) * DOC: Various fixes to "Running mriqc" section (nipreps#897) * MAINT: Updates to ``CONTRIBUTORS.md`` file * MAINT: Revise Docker image settings & CircleCI (nipreps#937) * MAINT: Finalize transfer to ``nipreps`` organization (nipreps#936) * MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org (nipreps#930) * MAINT: New Docker layer caching system of other *NiPreps* (nipreps#929) * MAINT: Code style overhaul (nipreps#901) * MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s (nipreps#924) * STY: Run ``black`` at the top of the repo (nipreps#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 (nipreps#938) * FIX: Revise building documentation at RTD after migration (nipreps#935) * FIX: Final touch-ups in the maintenance of Docker image + CI (nipreps#928) * FIX: Update unit tests (nipreps#927) * FIX: Update dependencies and repair BOLD workflow accordingly (nipreps#926) * FIX: Update dependencies and repair T1w workflow accordingly (nipreps#925) * FIX: Set ``matplotlib`` on ``Agg`` output mode (nipreps#892) * ENH: Refactored long strings to a :mod:`mriqc.messages` module (nipreps#901) * ENH: Refactored :mod:`mriqc.interfaces.common` module (nipreps#901) * DOC: Various fixes to "Running mriqc" section (nipreps#897) * MAINT: Revise Docker image settings & CircleCI (nipreps#937) * MAINT: Finalize transfer to ``nipreps`` organization (nipreps#936) * MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org (nipreps#930) * MAINT: New Docker layer caching system of other *NiPreps* (nipreps#929) * MAINT: Code style overhaul (nipreps#901) * MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s (nipreps#924) * STY: Run ``black`` at the top of the repo (nipreps#932)
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