Fmriprep

=========================
Bug-fix release in the 20.2.x LTS series.

This release includes some fixes to minor bugs, and includes enhancements
to allow the user to specify a different slice-timing-correction (STC) target.

Each BOLD series will contain ``SliceTimingCorrected`` metadata to indicate
whether STC was performed. If performed, the ``StartTime`` metadata field will
be set to indicate the onset time of the BOLD series.

* FIX: Avoid unnecessary connections based on branching logic (2508)
* FIX: Permit missing TR to show PyBIDS error at workflow construction time (2513)
* [BACKPORT] FIX: Catch FreeSurfer error related to FIPS being enabled (2490)
* ENH: Use ``BIDSLayoutIndexer`` and do not index unnecessary modalities (2494)
* [BACKPORT] ENH: Slice-timing correction improvements (2565)

======================
Patch release in the 20.2.x LTS series.
Addresses minimal problems in some edge-cases, overall improves the documentation and infrastructure.
Exercises some maintenance operations addressing problems surfaced when the previous tag 20.2.2 was released.

* FIX: Address the problems of a sloppy merge (2468)
* FIX: ``DerivativesDataSink`` nondeterministic checksums fixed with ``niworkflows=~1.3.4`` (2458)
* FIX: Address dependency incompatibilities by pinning specific packages (2463)
* FIX: Unprotected import of ``sentry_sdk``, which is not a dependency (2460)
* ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (2461)
* DOC: Transfer duplicated documentation to www.nipreps.org (2469)
* DOC: Better explanation on how spike regressors are generated (2465)
* DOC: Clarify that ``res-2`` entity does not mean 2mm (2466)
* MAINT: Containers - remove ``/root/.npm`` (2464)
* MAINT: Back port CircleCI configuration from dev branch (2456)

======================
Hot-fix release in the 20.2.x LTS series.
Addressing a bug on *fMRIPrep*'s resampling to standard spaces (2444).
In addition, some other relevant bug-fixes and performance improvements are built in this patch.

* FIX: Feed *NiTransforms* with LTAs of type RAS2RAS (2444)
* FIX: Add some clarity to ``BrokenProcessPool`` failures (2436)
* FIX: Fall-back to initializing workflow in main process (2435)
* FIX: Raise informative error when duplicate subworkflows are added (2434)
* FIX: Non-existing path or JSON syntax error for ``--bids-filter-file`` should raise on error (2331)
* FIX: Ignore SBRef files if ``--ignore sbref`` is passed (2370)
* ENH: Relax requirement for *PyBIDS* databases to exist (2429)
* ENH: Improve ``_get_series_len`` performance (2406)
* ENH: Set and track NumPy's random seed (2400)
* DOC: Skull-stripping is forced by default (2430)
* MAINT: Pin ``nilearn==0.6.2`` (2427)
* MAINT: Pin ``tedana==0.0.9a1`` for LTS branch (2403)
* MAINT: Failing CI (2401)

==========================
Bug-fix release in the 20.2.x LTS series.

This release adds missing metadata to GIFTI and CIFTI-2 derivatives and fixes a logging
bug affecting a small number of datasets.

Additionally the ``--output-layout bids`` flag will now output fMRIPrep derivatives directly
into the output directory, nesting FreeSurfer derivatives by default in
``<output>/sourcedata/freesurfer``. This layout allows the output root to be a valid BIDS
Derivatives dataset, simplifying data management and provenance tracking with content tracking
tools, such as `DataLad <https://handbook.datalad.org/>`__. This layout will likely become the
default in future release series.

* ENH: Output TaskName and timing metadata for all resampled BOLD series (2320)
* ENH: Add ``--output-layout`` CLI option to enable BIDS (YODA) mode (2303)
* ENH: Add Docker authentication to increase pull rate limit (2316)
* FIX: Specify logger for warning (2298)

===========================
With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

.. admonition:: Long-Term Support (LTS)

*fMRIPrep* 20.2 LTS introduces the `long-term support program
<https://www.nipreps.org/devs/releases/#long-term-support-series>`__.
This LTS version will be kindly steered and maintained by
the group of Dr. Basile Pinsard and Prof. Pierre Bellec at
`CRIUGM <https://criugm.qc.ca/>`__, (Université de Montréal).
The LTS is planned for a window of 4 years of support (i.e., until
September 2024).

.. caution::

As with all minor version increments, working directories
from previous versions **should not be reused**.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Pin *NiWorkflows* 1.3.1 and *sMRIPrep* 0.7.0rc2, including bugfix for INU-correction failures (nipreps/niworkflows567)
* FIX: Get missing ``probseg`` file from MNI152NLin2009cAsym (2271)
* FIX: Restore ``--ignore t2w/flair`` options (2260)
* FIX: Revise the reproducibility of *CompCor* masks (2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (2201)
* FIX: Storing ``--bids-filters`` within config file (2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (1803)
* FIX: *FreeSurfer* license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (2223)
* ENH: Reuse config (2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (2233)
* ENH: Leverage BIDSLayout's ``database_path`` (2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (2204)
* ENH: Report number of echoes in BOLD summary. (2184)
* ENH: Ensure *NiPype* telemetry is just pinged once (2168)
* DOC: Add FAQ entry for using pre-indexed layouts (2256)
* DOC: Update reference in "Refinement of Brain Mask" description (2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (2196)
* DOC: Update references to https://github.com/nipreps (#2191)
* DOC: Pin *NiPype* with new Sphinx extension syntax (2092)
* MAINT: Upgrade ANTs to 2.3.3 in ``Dockerfile`` (9512086)
* MAINT: Track 2269 and 2269, bug-fixes on the 20.1.x series
* MAINT: Remove derivatives from layout index ignores (2258)
* MAINT: Track 2252 from 20.1.x series (2253)
* MAINT: Silence *PyBIDS* warning by setting extension mode (2250)
* MAINT: Drop CircleCI docs build (2247)
* MAINT: Pin latest *NiPreps* (2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (2183)
* MAINT: Delete release-drafter (2169)
* MAINT: Track bug-fix release on the 20.1.x series (2165)
* MAINT: Remove auto-comment bot (2166)
* MAINT: Improve the questions on the bug-report template (2158)

.. admonition:: Author list for papers based on *fMRIPrep* 20.2 LTS 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 *fMRIPrep*.
To do so, please move the author(s) name(s) to the front of the following list:

Markiewicz, Christopher J. \ :sup:`1`\ ; Goncalves, Mathias \ :sup:`1`\ ; DuPre, Elizabeth \ :sup:`2`\ ; Kent, James D. \ :sup:`3`\ ; Salo, Taylor \ :sup:`4`\ ; Ciric, Rastko \ :sup:`1`\ ; Pinsard, Basile \ :sup:`5`\ ; Finc, Karolina \ :sup:`6`\ ; de la Vega, Alejandro \ :sup:`7`\ ; Feingold, Franklin \ :sup:`1`\ ; Tooley, Ursula A. \ :sup:`8`\ ; Benson, Noah C. \ :sup:`9`\ ; Urchs, Sebastian \ :sup:`2`\ ; Blair, Ross W. \ :sup:`1`\ ; Erramuzpe, Asier \ :sup:`10`\ ; Lurie, Daniel J. \ :sup:`11`\ ; Heinsfeld, Anibal S. \ :sup:`12`\ ; Jacoby, Nir \ :sup:`13`\ ; Jamison, Keith W. \ :sup:`14`\ ; Frederick, Blaise B. \ :sup:`15, 16`\ ; Valabregue, Romain \ :sup:`17`\ ; Sneve, Markus H. \ :sup:`18`\ ; Liem, Franz \ :sup:`19`\ ; Adebimpe, Azeez \ :sup:`20`\ ; Velasco, Pablo \ :sup:`21`\ ; Wexler, Joseph B. \ :sup:`1`\ ; Groen, Iris I. A. \ :sup:`22`\ ; Ma, Feilong \ :sup:`23`\ ; Amlien, Inge K. \ :sup:`18`\ ; Bellec, Pierre \ :sup:`5`\ ; Cieslak, Matthew \ :sup:`20`\ ; Devenyi, Grabriel A. \ :sup:`24`\ ; Ghosh, Satrajit S. \ :sup:`25, 26`\ ; Gomez, Daniel E. P. \ :sup:`27`\ ; Halchenko, Yaroslav O. \ :sup:`23`\ ; Isik, Ayse Ilkay \ :sup:`28`\ ; Moodie, Craig A. \ :sup:`1`\ ; Naveau, Mikaël \ :sup:`29`\ ; Rivera-Dompenciel, Adriana \ :sup:`3`\ ; Satterthwaite, Theodore D. \ :sup:`20`\ ; Sitek, Kevin R. \ :sup:`30`\ ; Stojić, Hrvoje \ :sup:`31`\ ; Thompson, William H. \ :sup:`1`\ ; Wright, Jessey \ :sup:`1`\ ; Ye, Zhifang \ :sup:`32`\ ; Gorgolewski, Krzysztof J. \ :sup:`1`\ ; Poldrack, Russell A. \ :sup:`1`\ ; Esteban, Oscar \ :sup:`33`\ .

Affiliations:

1. Department of Psychology, Stanford University
2. Montreal Neurological Institute, McGill University
3. Neuroscience Program, University of Iowa
4. Department of Psychology, Florida International University
5. SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada
6. Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń
7. University of Texas at Austin
8. Department of Neuroscience, University of Pennsylvania, PA, USA
9. Department of Psychology, New York University
10. Computational Neuroimaging Lab, BioCruces Health Research Institute
11. Department of Psychology, University of California, Berkeley
12. Child Mind Institute
13. Department of Psychology, Columbia University
14. Department of Radiology, Weill Cornell Medicine
15. McLean Hospital Brain Imaging Center, MA, USA
16. Consolidated Department of Psychiatry, Harvard Medical School, MA, USA
17. CENIR, INSERM U1127, CNRS UMR 7225, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
18. Center for Lifespan Changes in Brain and Cognition, University of Oslo
19. URPP Dynamics of Healthy Aging, University of Zurich
20. Perelman School of Medicine, University of Pennsylvania, PA, USA
21. Center for Brain Imaging, New York University
22. Department of Psychology, New York University, NY, USA
23. Dartmouth College: Hanover, NH, United States
24. Department of Psychiatry, McGill University
25. McGovern Institute for Brain Research, MIT, MA, USA
26. Department of Otolaryngology, Harvard Medical School, MA, USA
27. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen
28. Max Planck Institute for Empirical Aesthetics
29. Cyceron, UMS 3408 (CNRS - UCBN), France
30. Speech & Hearing Bioscience & Technology Program, Harvard University
31. Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London
32. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University
33. Department of Radiology, CHUV, Université de Lausanne

======================
Hotfix release addressing a bug on *fMRIPrep*'s resampling to standard spaces.
This release also includes some maintenance changes handling old versions of software.

* FIX: Feed *NiTransforms* with LTAs of type RAS2RAS (2444)
* MAINT: Pin ``svgutils==0.3.1`` for the 20.1.x series (2450)
* MAINT: Keep pip and setuptools with support for Python 3.5 (2449)
* MAINT: Some dependencies cannot be left unpinned (2446)