======================
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.
* FIX: Inconsistent API in anatomical CNR computation (`995 <https://github.com/nipreps/mriqc/pull/995>`__)
* FIX: Check sanity of input data before extracting IQMs (`994 <https://github.com/nipreps/mriqc/pull/994>`__)
* FIX: Plot segmentations after dropping off-diagonal (`989 <https://github.com/nipreps/mriqc/pull/989>`__)
* FIX: Replace all deprecated ``nibabel.get_data()`` in anatomical module (`988 <https://github.com/nipreps/mriqc/pull/988>`__)
* FIX: Resource profiler was broken with config file (`981 <https://github.com/nipreps/mriqc/pull/981>`__)
* FIX: preserve WM segments in rodents (`979 <https://github.com/nipreps/mriqc/pull/979>`__)
* FIX: Pin ``jinja2 < 3.1`` (`978 <https://github.com/nipreps/mriqc/pull/978>`__)
* FIX: Make toml config unique, works around 912 (`960 <https://github.com/nipreps/mriqc/pull/960>`__)
* FIX: Nipype multiproc plugin expects ``n_procs`` and not ``nprocs`` (`961 <https://github.com/nipreps/mriqc/pull/961>`__)
* FIX: Set TR when generating carpetplots (enables time for X axis) (`971 <https://github.com/nipreps/mriqc/pull/971>`__)
* FIX: ``template_resolution`` deprecation warning (`941 <https://github.com/nipreps/mriqc/pull/941>`__)
* FIX: Set entity ``datatype`` in ``BIDSLayout`` queries (`942 <https://github.com/nipreps/mriqc/pull/942>`__)
* FIX: T2w image of MNI template unavailable in Singularity (`940 <https://github.com/nipreps/mriqc/pull/940>`__)
* FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token (`938 <https://github.com/nipreps/mriqc/pull/938>`__)
* FIX: Revise building documentation at RTD after migration (`935 <https://github.com/nipreps/mriqc/pull/935>`__)
* FIX: Final touch-ups in the maintenance of Docker image + CI (`928 <https://github.com/nipreps/mriqc/pull/928>`__)
* FIX: Update unit tests (`927 <https://github.com/nipreps/mriqc/pull/927>`__)
* FIX: Update dependencies and repair BOLD workflow accordingly (`926 <https://github.com/nipreps/mriqc/pull/926>`__)
* FIX: Update dependencies and repair T1w workflow accordingly (`925 <https://github.com/nipreps/mriqc/pull/925>`__)
* FIX: Set ``matplotlib`` on ``Agg`` output mode (`892 <https://github.com/nipreps/mriqc/pull/892>`__)
* ENH: Deprecate ``--start-idx`` / ``--stop-idx`` (`993 <https://github.com/nipreps/mriqc/pull/993>`__)
* ENH: Add SynthStrip base module (`987 <https://github.com/nipreps/mriqc/pull/987>`__)
* ENH: Improve building workflow message feedback (`990 <https://github.com/nipreps/mriqc/pull/990>`__)
* ENH: Add instrumentation to monitor resources (`984 <https://github.com/nipreps/mriqc/pull/984>`__)
* ENH: Standalone, lightweight version of MultiProc plugin (`985 <https://github.com/nipreps/mriqc/pull/985>`__)
* ENH: Revise plugin and workflow initialization (`983 <https://github.com/nipreps/mriqc/pull/983>`__)
* ENH: Base generalization of the pipeline for rodents (`969 <https://github.com/nipreps/mriqc/pull/969>`__)
* ENH: Update to new *NiWorkflows*' API, which adds the crown to the carpetplot (`968 <https://github.com/nipreps/mriqc/pull/968>`__)
* ENH: Optimize *PyBIDS*' layout initialization (`939 <https://github.com/nipreps/mriqc/pull/939>`__)
* ENH: Refactored long strings to a :mod:`mriqc.messages` module (`901 <https://github.com/nipreps/mriqc/pull/901>`__)
* ENH: Refactored :mod:`mriqc.interfaces.common` module (`901 <https://github.com/nipreps/mriqc/pull/901>`__)
* DOC: Improve documentation of ``--nprocs`` and ``--omp-nthreads`` (`986 <https://github.com/nipreps/mriqc/pull/986>`__)
* DOC: Add ``sbatch`` file example for SLURM execution (`963 <https://github.com/nipreps/mriqc/pull/963>`__)
* DOC: Various fixes to "Running mriqc" section (`897 <https://github.com/nipreps/mriqc/pull/897>`__)
* MAINT: Refactor ``Dockerfile`` using new miniconda image (`974 <https://github.com/nipreps/mriqc/pull/974>`__)
* MAINT: Outsource the classifier into nipreps/mriqc-learn (`973 <https://github.com/nipreps/mriqc/pull/973>`__)
* MAINT: Update ``CONTRIBUTORS.md`` (`953 <https://github.com/nipreps/mriqc/pull/953>`__)
* MAINT: Update contributor location (`952 <https://github.com/nipreps/mriqc/pull/952>`__)
* MAINT: Updates to ``CONTRIBUTORS.md`` file
* MAINT: Revise Docker image settings & CircleCI (`937 <https://github.com/nipreps/mriqc/pull/937>`__)
* MAINT: Finalize transfer to ``nipreps`` organization (`936 <https://github.com/nipreps/mriqc/pull/936>`__)
* MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org (`930 <https://github.com/nipreps/mriqc/pull/930>`__)
* MAINT: New Docker layer caching system of other *NiPreps* (`929 <https://github.com/nipreps/mriqc/pull/929>`__)
* MAINT: Code style overhaul (`901 <https://github.com/nipreps/mriqc/pull/901>`__)
* MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s (`924 <https://github.com/nipreps/mriqc/pull/924>`__)
* STY: Run ``black`` at the top of the repo (`932 <https://github.com/nipreps/mriqc/pull/932>`__)
**Full Changelog**: https://github.com/nipreps/mriqc/compare/0.16.1...22.0.0
.. admonition:: Author list for papers based on *MRIQC* 22.0.x
As described in the `Contributor Guidelines
<https://www.nipreps.org/community/CONTRIBUTING/#recognizing-contributions>`__,
anyone listed as developer or contributor may write and submit manuscripts
about *MRIQC*.
To do so, please move the author(s) name(s) to the front of the following list:
Zvi Baratz \ :sup:`1`\ ; Christopher J. Markiewicz \ :sup:`2`\ ; Eilidh MacNicol \ :sup:`3`\ ; Dylan Nielson \ :sup:`4`\ ; Jan Varada \ :sup:`5`\ ; Ross W. Blair \ :sup:`2`\ ; William Triplett \ :sup:`6`\ ; Nikita Beliy \ :sup:`7`\ ; Céline Provins \ :sup:`8`\ ; John A. Lee \ :sup:`9`\ ; Ursula A. Tooley \ :sup:`10`\ ; James D. Kent \ :sup:`11`\ ; Bennet Fauber \ :sup:`12`\ ; Taylor Salo \ :sup:`13`\ ; Mathias Goncalves \ :sup:`2`\ ; Michael Krause \ :sup:`14`\ ; Pablo Velasco \ :sup:`15`\ ; Thomas Nichols \ :sup:`16`\ ; Adam Huffman \ :sup:`17`\ ; Johannes Achtzehn \ :sup:`18`\ ; Joke Durnez \ :sup:`2`\ ; Satrajit S. Ghosh \ :sup:`19`\ ; Asier Erramuzpe \ :sup:`20`\ ; Benjamin Kay \ :sup:`21`\ ; Daniel Birman \ :sup:`2`\ ; Michael G. Clark \ :sup:`22`\ ; Rafael Garcia-Dias \ :sup:`23`\ ; Sean Marret \ :sup:`5`\ ; Adam G. Thomas \ :sup:`24`\ ; Russell A. Poldrack \ :sup:`2`\ ; Krzysztof J. Gorgolewski \ :sup:`25`\ ; Oscar Esteban \ :sup:`26`\ .
Affiliations:
1. Sagol School of Neuroscience, Tel-Aviv University
2. Department of Psychology, Stanford University, CA, USA
3. Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
4. Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA
5. Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA
6. University of Florida: Gainesville, Florida, US
7. CRC ULiege, Liege, Belgium
8. Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
9. Quansight, Dublin, Ireland
10. Department of Neuroscience, University of Pennsylvania, PA, USA
11. Department of Psychology, University of Texas at Austin, TX, USA
12. University of Michigan, Ann Arbor, USA
13. Department of Psychology, Florida International University, FL, USA
14. Max Planck Institute for Human Development, Berlin, Germany
15. Center for Brain Imaging, New York University, NY, USA
16. Oxford Big Data Institute, University of Oxford, Oxford, GB
17. Department of Physics, Imperial College London, London, UK
18. Charité Berlin, Berlin, Germany
19. McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA
20. Computational Neuroimaging Lab, BioCruces Health Research Institute
21. Washington University School of Medicine, St.Louis, MO, USA
22. National Institutes of Health, USA
23. Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
24. Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
25. Google LLC
26. Department of Radiology, Lausanne University Hospital and University of Lausanne
Series 0.16.x
=============