Tags: nipreps/mriqc
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24.0.2 Release Notes ------------- A patch release with bugfixes and enhancements. CHANGES ------- * FIX: Pin latest *NiReports* release (24.0.2) addressing ``fMRIPlot`` issues by @oesteban (`#1342 <https://github.com/nipreps/mriqc/pull/1342>`__) * FIX: Edge artifacts in first and last slices due to interpolation by @oesteban (`#1338 <https://github.com/nipreps/mriqc/pull/1338>`__) * FIX: Normalize bids-filters' modality keys to be lowercase by @oesteban (`#1332 <https://github.com/nipreps/mriqc/pull/1332>`__) * ENH: Add license NOTICE to start banner by @oesteban (`#1343 <https://github.com/nipreps/mriqc/pull/1343>`__) * ENH: Enable writing crashfiles in compressed-pickle format by @oesteban (`#1339 <https://github.com/nipreps/mriqc/pull/1339>`__) * ENH: Use ``orjson`` to serialize JSON, addressing *Numpy* serialization issues by @oesteban (`#1337 <https://github.com/nipreps/mriqc/pull/1337>`__) * ENH: Handle WebAPI timeouts more gently by @oesteban (`#1336 <https://github.com/nipreps/mriqc/pull/1336>`__)
24.0.1 A patch release with a large number of bugfixes (mostly focusing on memory issues), maintenance activities, and the crawling of metadata before *Nipype* kicks in as a major optimization. With thanks to @jhlegarreta for his first contribution in `#1293 <https://github.com/nipreps/mriqc/pull/1293>__`. .. admonition:: Author list for papers based on *MRIQC* 24.0 series 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: Christopher J. Markiewicz \ :sup:`1`\ ; Zvi Baratz \ :sup:`2`\ ; Eilidh MacNicol \ :sup:`3`\ ; Céline Provins \ :sup:`4`\ ; Teresa Gomez \ :sup:`5`\ ; Dylan Nielson \ :sup:`6`\ ; Ross W. Blair \ :sup:`1`\ ; Jan Varada \ :sup:`7`\ ; Dimitri Papadopoulos Orfanos \ :sup:`8`\ ; William Triplett \ :sup:`9`\ ; Mathias Goncalves \ :sup:`1`\ ; Nikita Beliy \ :sup:`10`\ ; John A. Lee \ :sup:`11`\ ; Yibei Chen \ :sup:`12`\ ; Ursula A. Tooley \ :sup:`13`\ ; Patrick Sadil \ :sup:`14`\ ; Yaroslav O. Halchenko \ :sup:`15`\ ; James D. Kent \ :sup:`16`\ ; Taylor Salo \ :sup:`17`\ ; Bennet Fauber \ :sup:`18`\ ; Thomas Nichols \ :sup:`19`\ ; Pablo Velasco \ :sup:`20`\ ; Michael Krause \ :sup:`21`\ ; Jon Haitz Legarreta Gorroño \ :sup:`22`\ ; Satrajit S. Ghosh \ :sup:`23`\ ; Joke Durnez \ :sup:`1`\ ; Johannes Achtzehn \ :sup:`24`\ ; Elodie Savary \ :sup:`4`\ ; Adam Huffman \ :sup:`25`\ ; Rafael Garcia-Dias \ :sup:`26`\ ; Michael G. Clark \ :sup:`27`\ ; Michael Dayan \ :sup:`28`\ ; McKenzie P. Hagen \ :sup:`29`\ ; Daniel Birman \ :sup:`1`\ ; Benjamin Kay \ :sup:`30`\ ; Asier Erramuzpe \ :sup:`31`\ ; Adam C. Raikes \ :sup:`32`\ ; Adam G. Thomas \ :sup:`33`\ ; Russell A. Poldrack \ :sup:`1`\ ; Ariel Rokem \ :sup:`5`\ ; Oscar Esteban \ :sup:`4`\ . Affiliations: 1. Department of Psychology, Stanford University, CA, USA 2. Quantivly Inc., Somerville, MA, USA 3. Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK 4. Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland 5. The University of Washington eScience Institute, WA, USA 6. Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA 7. Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA 8. NeuroSpin, CEA, Université Paris-Saclay, NeuroSpin, Gif-sur-Yvette, France 9. University of Florida: Gainesville, Florida, US 10. CRC ULiege, Liege, Belgium 11. Quansight, Dublin, Ireland 12. McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, USA 13. Department of Neuroscience, University of Pennsylvania, PA, USA 14. Johns Hopkins Bloomberg School of Public Health, MD, USA 15. Psychological and Brain Sciences Department, Dartmouth College, NH, USA 16. Department of Psychology, University of Texas at Austin, TX, USA 17. Department of Psychology, Florida International University, FL, USA 18. University of Michigan, Ann Arbor, USA 19. Oxford Big Data Institute, University of Oxford, Oxford, GB 20. Center for Brain Imaging, New York University, NY, USA 21. Max Planck Institute for Human Development, Berlin, Germany 22. Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA 23. McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA 24. Charité Berlin, Berlin, Germany 25. Department of Physics, Imperial College London, London, UK 26. Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK 27. National Institutes of Health, USA 28. International Committee of the Red Cross - ICRC, Geneva, Switzerland 29. Psychology Department, University of Washington, Seattle, WA, USA 30. Washington University School of Medicine, St.Louis, MO, USA 31. Computational Neuroimaging Lab, BioCruces Health Research Institute 32. Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA 33. Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA CHANGES ------- * FIX: Multiecho fMRI crashing with 'unhashable type' errors by @oesteban in #1295 * FIX: Set ``n_procs`` instead of ``num_threads`` on node ``apply_hmc`` by @oesteban in #1309 * FIX: Address memory issues by limiting ``BigPlot``'s parallelization. by @oesteban in #1320 * FIX: Address memory issues in DWI pipeline by @oesteban in #1323 * FIX: Limit IQMs' node number of processes and therefore, memory by @oesteban in #1325 * FIX: Resolve numeric overflow in drift estimation node by @oesteban in #1324 * FIX: Revise bugfix #1324 by @oesteban in #1327 * FIX: Remove unreachable code within DWI pipeline by @oesteban in #1328 * ENH: Allow moving the cache folder with an environment variable by @oesteban in #1285 * ENH: Flatten multi-echo lists in circumstances that they fail by @oesteban in #1286 * ENH: Added type hints to config module by @zvi-quantivly in #1288 * ENH: Add test for the CLI parser by @jhlegarreta in #1293 * ENH: Add CLI entry point test by @jhlegarreta in #1294 * ENH: Add development dockerfile for testing local changes to repo. by @rwblair in #1299 * ENH: Crawl dataset's metadata only once and before Nipype's workflow by @oesteban in #1317 * ENH(dMRI): Deal gracefully with small CC masks by @oesteban in #1311 * ENH: Leverage new spun-off apply interface by @oesteban in #1313 * MAINT: Removed personal infromation from maintainers and updated in contributors by @zvi-quantivly in #1289 * MAINT: Add JHLegarreta to contributors list by @jhlegarreta in #1301 * MAINT: Flexibilize pandas pinned version by @oesteban in #1310 * MAINT: Remove *Pandas*'s ``FutureWarning`` by @oesteban in #1326 * DOC: Add description of ``summary_fg`` to the documentation by @celprov in #1306 * STY: Apply ruff/flake8-implicit-str-concat rule ISC001 by @DimitriPapadopoulos in #1296 * STY: Format *Jupyter notebooks* by @oesteban in #1321 **Full Changelog**: 24.0.0...24.0.1
24.0.0
Release Notes
-------------
Initial major release of 2024, featuring the **extraction of IQMs from
DWI data**
for first time in *MRIQC*'s timeline.
.. admonition:: Author list for papers based on *MRIQC* 23.0 series
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:
Christopher J. Markiewicz \ :sup:`1`\ ; Zvi Baratz \ :sup:`2`\ ;
Eilidh MacNicol \ :sup:`3`\ ; Céline Provins \ :sup:`4`\ ; Teresa Gomez
\ :sup:`5`\ ; Dylan Nielson \ :sup:`6`\ ; Jan Varada \ :sup:`7`\ ; Ross
W. Blair \ :sup:`1`\ ; Dimitri Papadopoulos Orfanos \ :sup:`8`\ ;
William Triplett \ :sup:`9`\ ; Mathias Goncalves \ :sup:`1`\ ; Nikita
Beliy \ :sup:`10`\ ; John A. Lee \ :sup:`11`\ ; Patrick Sadil \
:sup:`12`\ ; Ursula A. Tooley \ :sup:`13`\ ; Yibei Chen \ :sup:`14`\ ;
James D. Kent \ :sup:`15`\ ; Yaroslav O. Halchenko \ :sup:`16`\ ; Bennet
Fauber \ :sup:`17`\ ; Taylor Salo \ :sup:`18`\ ; Michael Krause \
:sup:`19`\ ; Pablo Velasco \ :sup:`20`\ ; Thomas Nichols \ :sup:`21`\ ;
Adam Huffman \ :sup:`22`\ ; Elodie Savary \ :sup:`4`\ ; Johannes
Achtzehn \ :sup:`23`\ ; Joke Durnez \ :sup:`1`\ ; Satrajit S. Ghosh \
:sup:`24`\ ; Adam C. Raikes \ :sup:`25`\ ; Asier Erramuzpe \ :sup:`26`\
; Benjamin Kay \ :sup:`27`\ ; Daniel Birman \ :sup:`1`\ ; McKenzie P.
Hagen \ :sup:`28`\ ; Michael Dayan \ :sup:`29`\ ; Michael G. Clark \
:sup:`30`\ ; Rafael Garcia-Dias \ :sup:`31`\ ; Adam G. Thomas \
:sup:`32`\ ; Russell A. Poldrack \ :sup:`1`\ ; Ariel Rokem \ :sup:`5`\ ;
Oscar Esteban \ :sup:`4`\ .
Affiliations:
1. Department of Psychology, Stanford University, CA, USA
2. Quantivly Inc., Somerville, MA, USA
3. Department of Neuroimaging, Institute of Psychiatry, Psychology
and Neuroscience, King's College London, London, UK
4. Department of Radiology, Lausanne University Hospital and
University of Lausanne, Switzerland
5. The University of Washington eScience Institute, WA, USA
6. Section on Clinical and Computational Psychiatry, National
Institute of Mental Health, Bethesda, MD, USA
7. Functional MRI Facility, National Institute of Mental Health,
Bethesda, MD, USA
8. NeuroSpin, CEA, Université Paris-Saclay, NeuroSpin,
Gif-sur-Yvette, France
9. University of Florida: Gainesville, Florida, US
10. CRC ULiege, Liege, Belgium
11. Quansight, Dublin, Ireland
12. Johns Hopkins Bloomberg School of Public Health, MD, USA
13. Department of Neuroscience, University of Pennsylvania, PA,
USA
14. McGovern Institute for Brain Research, Massachusetts Institute
of Technology, Cambridge, USA
15. Department of Psychology, University of Texas at Austin, TX,
USA
16. Psychological and Brain Sciences Department, Dartmouth
College, NH, USA
17. University of Michigan, Ann Arbor, USA
18. Department of Psychology, Florida International University,
FL, USA
19. Max Planck Institute for Human Development, Berlin, Germany
20. Center for Brain Imaging, New York University, NY, USA
21. Oxford Big Data Institute, University of Oxford, Oxford, GB
22. Department of Physics, Imperial College London, London, UK
23. Charité Berlin, Berlin, Germany
24. McGovern Institute for Brain Research, MIT, MA, USA; and
Department of Otolaryngology, Harvard Medical School, MA, USA
25. Center for Innovation in Brain Science, University of Arizona,
Tucson, AZ, USA
26. Computational Neuroimaging Lab, BioCruces Health Research
Institute
27. Washington University School of Medicine, St.Louis, MO, USA
28. Psychology Department, University of Washington, Seattle, WA,
USA
29. International Committee of the Red Cross - ICRC, Geneva,
Switzerland
30. National Institutes of Health, USA
31. Institute of Psychiatry, Psychology & Neuroscience, King's
College London, London, UK
32. Data Science and Sharing Team, National Institute of Mental
Health, Bethesda, MD, USA
CHANGES
-------
* FIX: Bug in *toml* loader crashing with mixed arrays in config (#1281)
* FIX: Remove *DataLad* as a node (#1278)
* FIX: Calculation of trivial shells (#1276)
* FIX: Finalized naming and connection of DWI IQMs (#1272)
* FIX: Enable group reports for DWI (#1266)
* FIX: Address issues that had broken the group reports (#1262)
* FIX: Select filters if modalities are selected (#1261)
* FIX: Make sure new logs and config file output are compatible with
parallel processes (#1259)
* FIX: Skip short BOLD runs that break outlier detection (#1120)
* FIX: Revise config save/load and update inputs after dropping (#1245)
* FIX: Drift should not be estimated when less than three low-b volumes
present (#1242, #1243)
* FIX: Handle ``NUMEXPR_MAX_THREADS`` like ``OMP_NUM_THREADS`` (#1241)
* FIX: Exclude DWI runs with insufficient orientations or missing bvals
(#1240)
* FIX: Avert costly ``BIDSLayout.__repr__`` calls when saving config
(#1239)
* FIX: Duplicate node in anatomical workflow (#1234)
* FIX: Typo in ``sorted(..., reverse=True)`` call (#1211)
* ENH: Fail for non-formatted code (#1274)
* ENH: Annotate nodes with ``n_procs`` to allow safe parallelization
(#1277)
* ENH: Mechanism to protect config's fields and write out config (#1258)
* ENH: Improve documentation and logging of *SynthStrip*'s model (#1254)
* ENH: Improve logging of runtime (#1253)
* ENH: Expose a command-line option for minimum DWI volumes (#1249)
* ENH: Improve error handling and logging (#1238)
* ENH: Add *b*-vector angular deviations as IQMs (#1233)
* ENH: Move from DTI to DKI with multishell data (#1230)
* ENH: Noise floor estimated with PCA (``dwidenoise``) as an IQM (#1229)
* ENH: Integrate PIESNO noise mask and sigma estimation (#1227)
* ENH: Use MAD for robust estimation of sigma in the CC mask (#1228)
* ENH: Add new IQM for DWI → NDC (#1226)
* ENH: Add FA-based IQMs (nans percentage and degenerate percentage)
(#1225)
* ENH: Add computation of spiking voxels mask and percent IQMs (#1224)
* ENH: Adds diffusion-related IQMs. (#1131)
* ENH: Revise summary stats extraction and include controlled roundings
(#1219)
* DOC: Add changelog to documentation (#1217)
* MAINT: Added ruff to development dependencies (#1271)
* MAINT: Removed pre-commit from development dependencies (#1269)
* MAINT: Clean up more ``FutureWarning`` issued by *Pandas* (#1257)
* MAINT: Prevent pandas-originating deprecation warning (#1251)
* MAINT: Move GitHub Actions and config files from *flake8* → *ruff*
(#1212)
* MAINT: Update contributor affiliation in ``CONTRIBUTORS.md`` (#1214)
* STY: Reformat diffusion workflows module (#1279)
* STY: Applied ruff formatting (#1273)
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