github nipreps/mriqc 26.1.1

one hour ago
  • Docker: docker pull nipreps/mriqc:26.1.1 (linux/amd64 and linux/arm64)
  • PyPI: pip install mriqc==26.1.1 (Python 3.13 or newer)

A patch release with bug fixes. Anatomical runs whose background is almost all zeros, as in many defaced and synthetic images, no longer crash in ComputeQI2, and the group level now honours the participant, session, run and task selection.

With thanks to @DimitriPapadopoulos for the zizmor security audit and the new ruff rules.

Changes in IQMs and reports

  • Anatomical runs where more than 99% of the background is exactly zero get qi_2 = 0 instead of crashing (#1493).
  • When the non-zero background voxels have a MAD of zero, no background voxel is flagged as an artifact anymore: qi_1 becomes 0, and summary_bg_*, snrd_* and cnr are computed on the full air mask (#1499).
  • DWI: snr_cc_shell<N>_* were computed one shell off (shell1 on the b=0 volumes, and the last shell was never reported). They now follow the diffusion-weighted shells, and sigma_piesno changes where many slices had a zero sigma (#1492).
  • Group reports label the FWHM in voxels for every modality, plot the average BOLD FWHM, and mark clipped FD and spikes points. No IQMs change (#1500).
  • A report no longer includes the figures of other acquisitions or runs of the same subject (#1498).

Changes in behavior

  • The default BIDS database moves from <output_dir>/.bids_db to <work_dir>/.bids_db. A database left in the output folder by an earlier version is ignored, not deleted, and a saved database that points to another dataset root is re-indexed with a warning (#1497).
  • At the group level, --participant-label, --session-id, --run-id, --task-id and --bids-filter-file limit the IQMs gathered. The filtered tables and reports keep the group_<suffix>.* names (#1496).
  • The group level no longer reads the raw data, so it runs on DataLad datasets whose content is not present (#1495).
  • DWI phase images (part-phase) are skipped unless a filter selects them, and --task-id works again (#1494).

Changes

  • FIX: Return QI2 = 0 when the background is almost all zeros by @oesteban (#1493)
  • FIX: Do not flag every background voxel as artifact when its MAD is zero by @oesteban (#1499)
  • FIX: Compute the corpus callosum SNR on the right DWI shells by @oesteban (#1492)
  • FIX: Make the group level honour the participant, session, run and task selection by @oesteban (#1496)
  • FIX: Run the group level without reading the raw data by @oesteban (#1495)
  • FIX: Re-index when the saved BIDS database points elsewhere, and keep it in the work directory by @oesteban (#1497)
  • FIX: Skip DWI phase images, and make --task-id work again by @oesteban (#1494)
  • FIX: Keep figures of other acquisitions out of a report by @oesteban (#1498)
  • FIX: Label FWHM in voxels, plot the BOLD average, and mark clipped FD points by @oesteban (#1500)
  • FIX: Make the integration IQM check fail on any changed value (dfcheck --strict) by @oesteban (#1491)
  • DOC: Document the DWI IQMs and how to run the tests by @oesteban (#1501)
  • DOC: Explain where container images look for TemplateFlow templates by @oesteban (#1509)
  • MAINT: Add @asaraog to CONTRIBUTORS.md by @oesteban (#1482)
  • MAINT: Update contributor affiliation for Ariel Rokem by @arokem (#1484)
  • MAINT: Bump actions/checkout to v7.0.1 and actions/setup-python to v7.1.0 by @dependabot (#1505, #1506)
  • STY: Enforce more ruff rules by @DimitriPapadopoulos (#1489)
  • CI: Add a zizmor GitHub Action for security auditing by @DimitriPapadopoulos (#1485)
  • CI: Pin actions by commit and clear the zizmor findings by @oesteban (#1502)
  • CI: Run DWI and FLAIR end to end on GitHub Actions by @oesteban (#1487)
  • CI: Republish the integration reports site when Integration succeeds by @oesteban (#1490)
Author list for papers based on MRIQC 26.1 series

As described in the Contributor Guidelines, anyone listed as a 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 1; Zvi Baratz 2; Céline Provins 3; Eilidh MacNicol 4; Dimitri Papadopoulos Orfanos 5; Teresa Gomez 6; Dylan Nielson 7; Jan Varada 8; Ross W. Blair 1; McKenzie P. Hagen 9; William Triplett 10; Jon Haitz Legarreta Gorroño 11; Mathias Goncalves 1; Nikita Beliy 12; John A. Lee 13; Patrick Sadil 14; Ursula A. Tooley 15; Yaroslav O. Halchenko 16; Yibei Chen 17; James D. Kent 18; Apoorv Saraogee 19; Bennet Fauber 20; Taylor Salo 21; Michael Krause 22; Pablo Velasco 23; Thomas Nichols 24; Victor Férat 25; Adam Huffman 26; Elodie Savary 3; Johannes Achtzehn 27; Joke Durnez 1; Satrajit S. Ghosh 28; Adam C. Raikes 29; Asier Erramuzpe 30; Benjamin Kay 31; Daniel Birman 1; Michael Dayan 32; Michael G. Clark 33; Rafael Garcia-Dias 34; Adam G. Thomas 35; Russell A. Poldrack 1; Ariel Rokem 36; Oscar Esteban 37.

Affiliations:

  1. Department of Psychology, Stanford University, CA, USA
  2. Quantivly Inc., Somerville, MA, USA
  3. Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland
  4. Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
  5. NeuroSpin, CEA, Université Paris-Saclay, NeuroSpin, Gif-sur-Yvette, France
  6. The University of Washington eScience Institute, WA, USA
  7. Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA
  8. Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA
  9. Psychology Department, University of Washington, Seattle, WA, USA
  10. University of Florida: Gainesville, Florida, US
  11. Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA
  12. CRC ULiege, Liege, Belgium
  13. Quansight, Dublin, Ireland
  14. Johns Hopkins Bloomberg School of Public Health, MD, USA
  15. Department of Neuroscience, University of Pennsylvania, PA, USA
  16. Psychological and Brain Sciences Department, Dartmouth College, NH, USA
  17. McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, USA
  18. Department of Psychology, University of Texas at Austin, TX, USA
  19. Independent researcher, San Jose, CA, USA
  20. University of Michigan, Ann Arbor, USA
  21. Department of Psychology, Florida International University, FL, USA
  22. Max Planck Institute for Human Development, Berlin, Germany
  23. Center for Brain Imaging, New York University, NY, USA
  24. Oxford Big Data Institute, University of Oxford, Oxford, GB
  25. Department of Basic Neurosciences, Université de Genève, Geneva, Switzerland
  26. Department of Physics, Imperial College London, London, UK
  27. Charité Berlin, Berlin, Germany
  28. McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA
  29. Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA
  30. Computational Neuroimaging Lab, BioCruces Health Research Institute
  31. Washington University School of Medicine, St.Louis, MO, USA
  32. International Committee of the Red Cross - ICRC, Geneva, Switzerland
  33. National Institutes of Health, USA
  34. Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
  35. Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
  36. Centre for Addiction and Mental Health and University of Toronto, Toronto, ON, Canada
  37. School of Engineering, HES-SO Valais/Wallis, Sion, Switzerland

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