Mriqc

========================
A patch release with a large number of bugfixes (mostly focusing on memory issues), maintenance
activities, and metadata crawling 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 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 \ :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 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 the 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 a development Dockerfile for testing local changes to the 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 information from maintainers and updated in contributors by zvi-quantivly in https://github.com/nipreps/mriqc/pull/1289
* MAINT: Add JHLegarreta to the 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

=======================
Initial major release of 2024, featuring the **extraction of IQMs from DWI data**
for the first time in *MRIQC*'s timeline.

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)

=======================
A long-overdue hotfix release addressing many bugs generated during the development
of the new dMRI workflows, and some relating to improvements of the handling of
multi-echo fMRI.
The release also include one year-worth of maintenance actions and a general code
cleanup with *Ruff*.

CHANGES
-------

* FIX: Missing connection to head-motion estimation node in DWI workflow by `oesteban <https://github.com/oesteban>`__ in `#1207 <https://github.com/nipreps/mriqc/pull/1207>`__
* FIX: Revise porting to ``Loader`` by `oesteban <https://github.com/oesteban>`__ in `#1201 <https://github.com/nipreps/mriqc/pull/1201>`__
* FIX: Revise the last two sloppy merges by `oesteban <https://github.com/oesteban>`__ in `#1200 <https://github.com/nipreps/mriqc/pull/1200>`__
* FIX: Move from ``pkg_resources`` to ``niworkflows.data.Loader`` by `oesteban <https://github.com/oesteban>`__ in `#1199 <https://github.com/nipreps/mriqc/pull/1199>`__
* FIX: DIPY not listed as a dependency by `oesteban <https://github.com/oesteban>`__ in `#1197 <https://github.com/nipreps/mriqc/pull/1197>`__
* FIX: Include ``dwidenoise`` within Docker image by `oesteban <https://github.com/oesteban>`__ in `#1196 <https://github.com/nipreps/mriqc/pull/1196>`__
* FIX: Copy name attribute of ``dataset_description.json`` from input dataset by `celprov <https://github.com/celprov>`__ in `#1187 <https://github.com/nipreps/mriqc/pull/1187>`__
* FIX: Remove FD as an ``iterfield`` in ``MapNode`` causing crash with ME-BOLD by `celprov <https://github.com/celprov>`__ in `#1179 <https://github.com/nipreps/mriqc/pull/1179>`__
* FIX: Incorrect plugin metadata passed to *Report Assembler* by `oesteban <https://github.com/oesteban>`__ in `#1188 <https://github.com/nipreps/mriqc/pull/1188>`__
* FIX: Temporary fix of the missing ``"dwi"`` key by `celprov <https://github.com/celprov>`__ in `#1174 <https://github.com/nipreps/mriqc/pull/1174>`__
* FIX: Rearrange multi-echo report by `celprov <https://github.com/celprov>`__ in `#1164 <https://github.com/nipreps/mriqc/pull/1164>`__
* FIX: Typo in ``inputnode`` field in dMRI masking workflow by `celprov <https://github.com/celprov>`__ in `#1165 <https://github.com/nipreps/mriqc/pull/1165>`__
* FIX: Bug in group level workflow by `celprov <https://github.com/celprov>`__ in `#1148 <https://github.com/nipreps/mriqc/pull/1148>`__
* FIX: Bugs in DWI workflow by `celprov <https://github.com/celprov>`__ in `#1147 <https://github.com/nipreps/mriqc/pull/1147>`__
* FIX: Use simpler DWI reference workflow by `yibeichan <https://github.com/yibeichan>`__ in `#1145 <https://github.com/nipreps/mriqc/pull/1145>`__
* FIX: Drop deprecated *Networkx*'s API by `celprov <https://github.com/celprov>`__ in `#1137 <https://github.com/nipreps/mriqc/pull/1137>`__
* FIX: Replace ``np.float`` by ``np.float64`` by `celprov <https://github.com/celprov>`__ in `#1140 <https://github.com/nipreps/mriqc/pull/1140>`__
* ENH: Improved logging and optimize early checkpoint on subjects by `oesteban <https://github.com/oesteban>`__ in `#1198 <https://github.com/nipreps/mriqc/pull/1198>`__
* ENH: Store confound timeseries data by `psadil <https://github.com/psadil>`__ in `#1166 <https://github.com/nipreps/mriqc/pull/1166>`__
* ENH: Large overhaul of the functional workflow w/focus on ME-EPI by `oesteban <https://github.com/oesteban>`__ in `#1155 <https://github.com/nipreps/mriqc/pull/1155>`__
* ENH: Implement BIDS filters file and drop legacy BIDS querying by `oesteban <https://github.com/oesteban>`__ in `#1154 <https://github.com/nipreps/mriqc/pull/1154>`__
* ENH: Swap background and zoomed-in visualizations in anatomical reports by `oesteban <https://github.com/oesteban>`__ in `#1151 <https://github.com/nipreps/mriqc/pull/1151>`__
* MAINT: Test on *Python* 3.12 by `DimitriPapadopoulos <https://github.com/DimitriPapadopoulos>`__ in `#1156 <https://github.com/nipreps/mriqc/pull/1156>`__
* MAINT: Disable flaky T1w test on CircleCI by `oesteban <https://github.com/oesteban>`__ in `#1202 <https://github.com/nipreps/mriqc/pull/1202>`__
* MAINT: Overhaul of the ``Dockerfile`` by `oesteban <https://github.com/oesteban>`__ in `#1195 <https://github.com/nipreps/mriqc/pull/1195>`__
* MAINT: Revise package's extra dependencies by `oesteban <https://github.com/oesteban>`__ in `#1194 <https://github.com/nipreps/mriqc/pull/1194>`__
* MAINT: Clean up some ``setuptools_scm`` remnants by `oesteban <https://github.com/oesteban>`__ in `#1193 <https://github.com/nipreps/mriqc/pull/1193>`__
* MAINT: Load ``FMRISummary`` from *NiReports* rather than *NiWorkflows* by `celprov <https://github.com/celprov>`__ in `#1167 <https://github.com/nipreps/mriqc/pull/1167>`__
* MAINT: Update to latest *migas*' API by `mgxd <https://github.com/mgxd>`__ in `#1160 <https://github.com/nipreps/mriqc/pull/1160>`__
* MAINT: Update bold to large resource class in ``config.yml`` by `oesteban <https://github.com/oesteban>`__ in `#1158 <https://github.com/nipreps/mriqc/pull/1158>`__
* MAINT: Refresh cached intermediate results by `oesteban <https://github.com/oesteban>`__ in `#1143 <https://github.com/nipreps/mriqc/pull/1143>`__
* MAINT: Simplify GitHub actions checks and update action versions by `effigies <https://github.com/effigies>`__ in `#1141 <https://github.com/nipreps/mriqc/pull/1141>`__
* MAINT: Python 3.11 is supported by `DimitriPapadopoulos <https://github.com/DimitriPapadopoulos>`__ in `#1123 <https://github.com/nipreps/mriqc/pull/1123>`__
* MAINT: Apply suggestions from pyupgrade by `DimitriPapadopoulos <https://github.com/DimitriPapadopoulos>`__ in `#1124 <https://github.com/nipreps/mriqc/pull/1124>`__
* DOC: Update *Sphinx* pinned version to 5 by `oesteban <https://github.com/oesteban>`__ in `#1192 <https://github.com/nipreps/mriqc/pull/1192>`__
* DOC: http:// → https:// by `DimitriPapadopoulos <https://github.com/DimitriPapadopoulos>`__ in `#1126 <https://github.com/nipreps/mriqc/pull/1126>`__
* DOC: Add info on the *FreeSurfer* requirement for bare install to address 1034 by `neurorepro <https://github.com/neurorepro>`__ in `#1130 <https://github.com/nipreps/mriqc/pull/1130>`__
* STY: Add *Ruff* config and fix all warnings and errors by `oesteban <https://github.com/oesteban>`__ in `#1203 <https://github.com/nipreps/mriqc/pull/1203>`__
* STY: Remove extraneous parentheses by `DimitriPapadopoulos <https://github.com/DimitriPapadopoulos>`__ in `#1186 <https://github.com/nipreps/mriqc/pull/1186>`__
* STY: Apply a few refurb suggestions by `DimitriPapadopoulos <https://github.com/DimitriPapadopoulos>`__ in `#1162 <https://github.com/nipreps/mriqc/pull/1162>`__
* STY: Fix typo found by codespell by `DimitriPapadopoulos <https://github.com/DimitriPapadopoulos>`__ in `#1161 <https://github.com/nipreps/mriqc/pull/1161>`__

======================
A new minor release featuring the new individual reports built with the new
*NiReports* VRS (visual reports system). This means *MRIQC* now uses the same
package *fMRIPrep* uses for generating its reports. In addition to that,
this new release also features *Beta* support for diffusion MRI (dMRI).

CHANGES
-------

* FIX: Better handling of BIDS cached indexation (`1121 <https://github.com/nipreps/mriqc/pull/1121>`__)
* FIX: Make doctest of ``NumberOfShells`` more reliable (`1122 <https://github.com/nipreps/mriqc/pull/1122>`__)
* FIX: Add protection for NaNs and INFs when calculating QI2 (`1112 <https://github.com/nipreps/mriqc/pull/1112>`__)
* FIX: ``PlotMosaic`` expects lists, not tuples (`1111 <https://github.com/nipreps/mriqc/pull/1111>`__)
* FIX: BIDS database directory handling (`1110 <https://github.com/nipreps/mriqc/pull/1110>`__)
* FIX: Remove unused dipy import in the functional interfaces (`1109 <https://github.com/nipreps/mriqc/pull/1109>`__)
* FIX: Refine the head mask after removal of FSL BET (`1107 <https://github.com/nipreps/mriqc/pull/1107>`__)
* FIX: Inform *SynthStrip* about the desired intraop threads (`1101 <https://github.com/nipreps/mriqc/pull/1101>`__)
* FIX: Test broken by 1098 (`1100 <https://github.com/nipreps/mriqc/pull/1100>`__)
* FIX: Separate report bootstrap files (anat vs. func) (`1098 <https://github.com/nipreps/mriqc/pull/1098>`__)
* FIX: Propagate logging level to subprocesses (`1030 <https://github.com/nipreps/mriqc/pull/1030>`__)
* ENH: Incorporate new NiReports' DWI heatmaps (`1119 <https://github.com/nipreps/mriqc/pull/1119>`__)
* ENH: More compact of shell-wise summary statistic maps (avg/std) (`1116 <https://github.com/nipreps/mriqc/pull/1116>`__)
* ENH: Add a basic DTI fitting into the diffusion workflow (`1115 <https://github.com/nipreps/mriqc/pull/1115>`__)
* ENH: MRIQC for DWI (`1113 <https://github.com/nipreps/mriqc/pull/1113>`__)
* ENH: Culminate dropping FSL as a dependency (`1108 <https://github.com/nipreps/mriqc/pull/1108>`__)
* ENH: Replace FSL FAST with ANTs Atropos for brain tissue segmentation (`1099 <https://github.com/nipreps/mriqc/pull/1099>`__)
* ENH: Drop FSL MELODIC (without alternative) (`1106 <https://github.com/nipreps/mriqc/pull/1106>`__)
* ENH: Drop FSL BET to estimate the "outskin" (head) mask (`1105 <https://github.com/nipreps/mriqc/pull/1105>`__)
* ENH: Drop utilization of "head" mask from template (`1104 <https://github.com/nipreps/mriqc/pull/1104>`__)
* ENH: Move templates' probsegs into individual at normalization (`1103 <https://github.com/nipreps/mriqc/pull/1103>`__)
* ENH: Improving the resource monitor -- infer PID from process name (`1049 <https://github.com/nipreps/mriqc/pull/1049>`__) (`#1049 <https://github.com/nipreps/mriqc/pull/1049>`__)
* ENH: Refactor reports system to use *NiReports* and the general VRS (`1085 <https://github.com/nipreps/mriqc/pull/1085>`__)
* MAINT: Move codespell configuration to ``pyproject.toml`` (`1097 <https://github.com/nipreps/mriqc/pull/1097>`__)
* MAINT: Update deprecated ``nibabel.spatialimage.get_data()`` calls (`1096 <https://github.com/nipreps/mriqc/pull/1096>`__)

.. 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:

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`\ ; Céline Provins \ :sup:`6`\ ; William Triplett \ :sup:`7`\ ; Mathias Goncalves \ :sup:`2`\ ; Nikita Beliy \ :sup:`8`\ ; John A. Lee \ :sup:`9`\ ; Ursula A. Tooley \ :sup:`10`\ ; James D. Kent \ :sup:`11`\ ; Yaroslav O. Halchenko \ :sup:`12`\ ; Bennet Fauber \ :sup:`13`\ ; Taylor Salo \ :sup:`14`\ ; Michael Krause \ :sup:`15`\ ; Pablo Velasco \ :sup:`16`\ ; Thomas Nichols \ :sup:`17`\ ; Adam Huffman \ :sup:`18`\ ; Elodie Savary \ :sup:`6`\ ; Johannes Achtzehn \ :sup:`19`\ ; Joke Durnez \ :sup:`2`\ ; Satrajit S. Ghosh \ :sup:`20`\ ; Asier Erramuzpe \ :sup:`21`\ ; Benjamin Kay \ :sup:`22`\ ; Daniel Birman \ :sup:`2`\ ; McKenzie P. Hagen \ :sup:`23`\ ; Michael G. Clark \ :sup:`24`\ ; Patrick Sadil \ :sup:`25`\ ; Rafael Garcia-Dias \ :sup:`26`\ ; Adam G. Thomas \ :sup:`27`\ ; Russell A. Poldrack \ :sup:`2`\ ; Ariel Rokem \ :sup:`28`\ ; Oscar Esteban \ :sup:`6`\ .

Affiliations:

1. Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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. Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland
7. University of Florida: Gainesville, Florida, US
8. CRC ULiege, Liege, Belgium
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. Psychological and Brain Sciences Department, Dartmouth College, NH, USA
13. University of Michigan, Ann Arbor, USA
14. Department of Psychology, Florida International University, FL, USA
15. Max Planck Institute for Human Development, Berlin, Germany
16. Center for Brain Imaging, New York University, NY, USA
17. Oxford Big Data Institute, University of Oxford, Oxford, GB
18. Department of Physics, Imperial College London, London, UK
19. Charité Berlin, Berlin, Germany
20. McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA
21. Computational Neuroimaging Lab, BioCruces Health Research Institute
22. Washington University School of Medicine, St.Louis, MO, USA
23. Psychology Department, University of Washington, Seattle, WA, USA
24. National Institutes of Health, USA
25. Johns Hopkins Bloomberg School of Public Health, MD, USA
26. Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
27. Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
28. The University of Washington eScience Institute, WA, USA

=======================
A hotfix release resolving a reggression introduced with the new optimized indexing.

* FIX: Underspecified regex sets ``BIDSLayout`` to ignore data with sessions (`1094 <https://github.com/nipreps/mriqc/pull/1094>`__)
* FIX: Input data has incompatible dimensionality (plotting ICA) (`1082 <https://github.com/nipreps/mriqc/pull/1082>`__)
* ENH: Optimize metadata gathering reusing ``BIDSLayout`` db (`1084 <https://github.com/nipreps/mriqc/pull/1084>`__)
* DOC : update anatomical example report in documentation (`1088 <https://github.com/nipreps/mriqc/pull/1088>`__)
* MAINT: Drop old ``mriqc_plot`` script (`1091 <https://github.com/nipreps/mriqc/pull/1091>`__)

=======================
The new 23.0.x series include several prominent changes.
Visualization has been migrated from *MRIQC* and *niworkflows* over to the new *NiReports* project.
This series include a major bugfix with **the optimization of the indexing** of the input BIDS folder,
which was taking large times with sizeable datasets.
Telemetry has also been incorporated with *migas*.
These new series also involve maintenance housekeeping, and includes some relevant bugfixes.

New contributors
----------------

* `arokem <https://github.com/arokem>`__ made their first contribution in `#1040 <https://github.com/nipreps/mriqc/pull/1040>`__
* `yarikoptic <https://github.com/yarikoptic>`__ made their first contribution in `#1057 <https://github.com/nipreps/mriqc/pull/1057>`__
* `esavary <https://github.com/esavary>`__ made their first contribution in `#1047 <https://github.com/nipreps/mriqc/pull/1047>`__

CHANGES
-------
**Full Changelog**: https://github.com/nipreps/mriqc/compare/22.0.6...23.0.0

* FIX: Send metadata extraction to workers (functional workflow) (`1081 <https://github.com/nipreps/mriqc/pull/1081>`__)
* FIX: Plot coronal as main plain for mosaic of rodent images (`1027 <https://github.com/nipreps/mriqc/pull/1027>`__)
* FIX: Address non-empty take from empty axes (anatomical IQMs) (`1077 <https://github.com/nipreps/mriqc/pull/1077>`__)
* FIX: Uniformize building workflow message (anat vs. func) (`1072 <https://github.com/nipreps/mriqc/pull/1072>`__)
* FIX: Move telemetry atexit into entrypoint func (`1067 <https://github.com/nipreps/mriqc/pull/1067>`__)
* FIX: Preempt PyBIDS to spend time indexing non-BIDS folders (`1050 <https://github.com/nipreps/mriqc/pull/1050>`__)
* FIX: Update T1w metrics (`1063 <https://github.com/nipreps/mriqc/pull/1063>`__)
* FIX: Resource monitor would not ever start tracking (`1051 <https://github.com/nipreps/mriqc/pull/1051>`__)
* ENH: Add DataLad getter to inputs of functional workflows (`1071 <https://github.com/nipreps/mriqc/pull/1071>`__)
* ENH: Add migas telemetry (`1036 <https://github.com/nipreps/mriqc/pull/1036>`__)
* ENH: Add codespell automation: config, action, and typos fixed (`1057 <https://github.com/nipreps/mriqc/pull/1057>`__)
* MAINT: Update *NiReports* calls to upcoming interfaces API (`1078 <https://github.com/nipreps/mriqc/pull/1078>`__)
* MAINT: Pacify codespell (`1080 <https://github.com/nipreps/mriqc/pull/1080>`__)
* MAINT: Conclude porting of reportlets into *NiReports* (`1068 <https://github.com/nipreps/mriqc/pull/1068>`__)
* MAINT: Migrate to hatchling (`1070 <https://github.com/nipreps/mriqc/pull/1070>`__)
* MAINT: Pin PyBIDS 0.15.6 (culminating 1050) (`1069 <https://github.com/nipreps/mriqc/pull/1069>`__)
* MAINT: Update niworkflows pin to support newer ANTs releases (`1047 <https://github.com/nipreps/mriqc/pull/1047>`__)
* MAINT: Fix minor aspects of WebAPI deployment on CircleCI (`1064 <https://github.com/nipreps/mriqc/pull/1064>`__)
* MAINT: Update CircleCI executor and use built-in docker-compose (`1061 <https://github.com/nipreps/mriqc/pull/1061>`__)
* MAINT: Rotate CircleCI secrets and setup up org-level context (`1046 <https://github.com/nipreps/mriqc/pull/1046>`__)
* DOC: Update documentation with the new carpet plot (`1045 <https://github.com/nipreps/mriqc/pull/1045>`__)
* DOC: Complete the documentation of ``summary_stats()`` (`1044 <https://github.com/nipreps/mriqc/pull/1044>`__)
* DOC: Fixes a couple of broken links to the *nipype* documentation (`1040 <https://github.com/nipreps/mriqc/pull/1040>`__)

.. 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:

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`\ ; Céline Provins \ :sup:`6`\ ; William Triplett \ :sup:`7`\ ; Mathias Goncalves \ :sup:`2`\ ; Nikita Beliy \ :sup:`8`\ ; John A. Lee \ :sup:`9`\ ; Ursula A. Tooley \ :sup:`10`\ ; James D. Kent \ :sup:`11`\ ; Yaroslav O. Halchenko \ :sup:`12`\ ; Bennet Fauber \ :sup:`13`\ ; Taylor Salo \ :sup:`14`\ ; Michael Krause \ :sup:`15`\ ; Pablo Velasco \ :sup:`16`\ ; Thomas Nichols \ :sup:`17`\ ; Adam Huffman \ :sup:`18`\ ; Johannes Achtzehn \ :sup:`19`\ ; Joke Durnez \ :sup:`2`\ ; Satrajit S. Ghosh \ :sup:`20`\ ; Asier Erramuzpe \ :sup:`21`\ ; Benjamin Kay \ :sup:`22`\ ; Daniel Birman \ :sup:`2`\ ; Elodie Savary \ :sup:`23`\ ; McKenzie P. Hagen \ :sup:`24`\ ; Michael G. Clark \ :sup:`25`\ ; Patrick Sadil \ :sup:`26`\ ; Rafael Garcia-Dias \ :sup:`27`\ ; Adam G. Thomas \ :sup:`28`\ ; Russell A. Poldrack \ :sup:`2`\ ; Ariel Rokem \ :sup:`29`\ ; Oscar Esteban \ :sup:`30`\ .

Affiliations:

1. Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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. Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
7. University of Florida: Gainesville, Florida, US
8. CRC ULiege, Liege, Belgium
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. Psychological and Brain Sciences Department, Dartmouth College, NH, USA
13. University of Michigan, Ann Arbor, USA
14. Department of Psychology, Florida International University, FL, USA
15. Max Planck Institute for Human Development, Berlin, Germany
16. Center for Brain Imaging, New York University, NY, USA
17. Oxford Big Data Institute, University of Oxford, Oxford, GB
18. Department of Physics, Imperial College London, London, UK
19. Charité Berlin, Berlin, Germany
20. McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA
21. Computational Neuroimaging Lab, BioCruces Health Research Institute
22. Washington University School of Medicine, St.Louis, MO, USA
23. Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland
24. Psychology Department, University of Washington, Seattle, WA, USA
25. National Institutes of Health, USA
26. Johns Hopkins Bloomberg School of Public Health, MD, USA
27. Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
28. Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
29. The University of Washington eScience Institute, WA, USA
30. Department of Radiology, Lausanne University Hospital and University of Lausanne