From 5c3f8b6ebbc388acbcc32f29b25f5e6757e20473 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 20 Aug 2024 11:31:27 +0200 Subject: [PATCH] rel(24.0.1): Update ``CHANGES.rst`` [skip ci] --- CHANGES.rst | 88 ++++++++++++++++++++++++++++++++++++++--------------- 1 file changed, 63 insertions(+), 25 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index 71fa3d89b..40a3db67e 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,9 +1,11 @@ -24.0.0 (April 17, 2024) -======================= -Initial major release of 2024, featuring the **extraction of IQMs from DWI data** -for first time in *MRIQC*'s timeline. +24.0.1 (August 20, 2024) +======================== +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. -.. admonition:: Author list for papers based on *MRIQC* 23.0 series +With thanks to @jhlegarreta for his first contribution in `#1293 __`. + +.. admonition:: Author list for papers based on *MRIQC* 24.0 series As described in the `Contributor Guidelines `__, @@ -11,7 +13,7 @@ for first time in *MRIQC*'s timeline. 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`\ . + 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: @@ -26,27 +28,63 @@ for first time in *MRIQC*'s timeline. 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 + 12. McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, 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 + 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. 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 + 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 https://github.com/nipreps/mriqc/pull/1295 +* FIX: Set ``n_procs`` instead of ``num_threads`` on node ``apply_hmc`` by @oesteban in https://github.com/nipreps/mriqc/pull/1309 +* FIX: Address memory issues by limiting ``BigPlot``'s parallelization. by @oesteban in https://github.com/nipreps/mriqc/pull/1320 +* FIX: Address memory issues in DWI pipeline by @oesteban in https://github.com/nipreps/mriqc/pull/1323 +* FIX: Limit IQMs' node number of processes and therefore, memory by @oesteban in https://github.com/nipreps/mriqc/pull/1325 +* FIX: Resolve numeric overflow in drift estimation node by @oesteban in https://github.com/nipreps/mriqc/pull/1324 +* FIX: Revise bugfix #1324 by @oesteban in https://github.com/nipreps/mriqc/pull/1327 +* FIX: Remove unreachable code within DWI pipeline by @oesteban in https://github.com/nipreps/mriqc/pull/1328 +* ENH: Allow moving the cache folder with an environment variable by @oesteban in https://github.com/nipreps/mriqc/pull/1285 +* ENH: Flatten multi-echo lists in circumstances that they fail by @oesteban in https://github.com/nipreps/mriqc/pull/1286 +* ENH: Added type hints to config module by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1288 +* ENH: Add test for the CLI parser by @jhlegarreta in https://github.com/nipreps/mriqc/pull/1293 +* ENH: Add CLI entry point test by @jhlegarreta in https://github.com/nipreps/mriqc/pull/1294 +* ENH: Add development dockerfile for testing local changes to repo. by @rwblair in https://github.com/nipreps/mriqc/pull/1299 +* ENH: Crawl dataset's metadata only once and before Nipype's workflow by @oesteban in https://github.com/nipreps/mriqc/pull/1317 +* ENH(dMRI): Deal gracefully with small CC masks by @oesteban in https://github.com/nipreps/mriqc/pull/1311 +* ENH: Leverage new spun-off apply interface by @oesteban in https://github.com/nipreps/mriqc/pull/1313 +* MAINT: Removed personal infromation from maintainers and updated in contributors by @zvi-quantivly in https://github.com/nipreps/mriqc/pull/1289 +* MAINT: Add JHLegarreta to contributors list by @jhlegarreta in https://github.com/nipreps/mriqc/pull/1301 +* MAINT: Flexibilize pandas pinned version by @oesteban in https://github.com/nipreps/mriqc/pull/1310 +* MAINT: Remove *Pandas*'s ``FutureWarning`` by @oesteban in https://github.com/nipreps/mriqc/pull/1326 +* DOC: Add description of ``summary_fg`` to the documentation by @celprov in https://github.com/nipreps/mriqc/pull/1306 +* STY: Apply ruff/flake8-implicit-str-concat rule ISC001 by @DimitriPapadopoulos in https://github.com/nipreps/mriqc/pull/1296 +* STY: Format *Jupyter notebooks* by @oesteban in https://github.com/nipreps/mriqc/pull/1321 + +**Full Changelog**: https://github.com/nipreps/mriqc/compare/24.0.0...24.0.1 + +24.0.0 (April 17, 2024) +======================= +Initial major release of 2024, featuring the **extraction of IQMs from DWI data** +for first time in *MRIQC*'s timeline. CHANGES -------