20.2.1 (Long-Term Support)

Release Notes

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. This layout will likely become the default in future release series.

Changes

• 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)

20.2.0 (Long-Term Support)

Release Notes

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.

fMRIPrep 20.2 LTS introduces the long-term support program. This LTS version will be kindly steered and maintained by the group of Dr. Basile Pinsard and Prof. Pierre Bellec at CRIUGM, (Université de Montréal). The LTS is planned for a window of 4 years of support (i.e., until September 2024).

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!

CHANGES

• FIX: Pin NiWorkflows 1.3.1 and sMRIPrep 0.7.0rc2, including bugfix for INU-correction failures (nipreps/niworkflows#567)
• 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)

20.2.0rc2

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 <http://www.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/niworkflows#567)
* 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)

20.2.0rc1

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 <http://www.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: 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: 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

20.1.3

Release Notes

Bug-fix release in the 20.1.x series.

CHANGES

• FIX: Dependency conflict between NiWorkflows and TemplateFlow (#2269)
• FIX: More targetted TemplateFlow queries to work with all later releases (#2268)
• MAINT: Update dependency pinnings including niworkflows~=1.2.9 and three minimal bug-fixes.

20.2.0rc0

Release Notes

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.

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!

CHANGES

• 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: 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: 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)

20.1.2

Release Notes

Bug-fix release in the 20.1.x series.

CHANGES

• FIX: Revise confounds in confounds-correlation plots (#2252)
• FIX: Coerce license path to pathlike (#2180)
• DOC: Update new sMRIPrep location (#2211)

20.1.1

Release Notes

Bug-fix release in the 20.1.x series.

CHANGES

• FIX: FreeSurfer license manipulation & canary (#2165)
• FIX: Dismiss echo entity from SDC reports (#2160)
• FIX: Ensure the command-line alias of --nprocs is respected (#2152)
• MAINT: Use legacy pip/setuptools for py2 checking (#2156)

20.1.0

The second minor release series of 2020 is finally here!

Release Notes

fMRIPrep 20.1.0 introduces a magnitude of new features and improvements. Originally nominated to become the first LTS (long-term support) version of fMRIPrep, this release has been supercharged with many new features and bug-fixes. To ensure long-term stability, we have postponed the LTS nomination to 20.2 to allow us unlocking the 20.1 earlier, and a more extensive stress testing of the series before jumping into a longer support commitment. Some key additions in this release include:

• A centralized configuration module keeping track of fMRIPrep's many options and run-time and environmental circumstances and settings. The new config module, which has been also propagated to other NiPreps dMRIPrep, MRIQC), comes to robustify the run-to-run replicability of fMRIPrep (e.g., tracking random seeds), make the option handling more modular but consistent (e.g., setting the ground for a command-line interface built off of the config module), and ease troubleshooting and telemetry.
• The anatomical preprocessing fast-track: a new experimental command-line option (--anat-derivatives <PATH>) checks that all necessary anatomical derivatives required by fMRIPrep are present under <PATH>, and skips the anatomical processing in full if fMRIPrep's expectations are met. Because now functional processing of many sessions and runs can be efficiently split into more digestible computational units (i.e., cluster job) while guaranteeing the exact same anatomical results are being used, this can significantly speed up longitudinal study preprocessing, and it is a fundamental optimization to process databases of densely scanned individuals such as My Connectome. This option is not recommended for single-session processing.
• A change in output CIFTI2 subcortical volume orientation to be compatible with HCP Pipeline tools and data.

Thanks

With thanks to Basile Pinsard, Joe B. Wexler, Noah Benson, and Marc Bue for contributions.

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!

CHANGES

• FIX: MultiLabel interpolations should not use float=True (#2147)
• FIX: Generate proper LTA transform prior BOLD sampling on surfaces (#2146)
• FIX: Temporary config file in work directory gets clobbered in parallel jobs (#2138)
• FIX: Dismiss echo entity on several derivatives and figures outputs (#2133)
• FIX: Correct summary report when using previously run recon-all (#2124)
• FIX: Ensure correct WM and CSF masks are picked in confounds workflow (#2128)
• FIX: Explicitly add default native resolution to volumetric outputs (nipreps/niworkflows#494)
• ENH: Finish the upstreaming of NiTransforms interfaces to NiWorkflows (#2132)
• ENH: Enable filtering for ANY or NONE in --bids-filter-file (#2123)
• ENH: Use new DerivativesDataSink from NiWorkflows 1.2.0 (#2114)
• ENH: Config module (#2018)
• ENH: Add option to ignore T2w / FLAIR images (#2015)
• ENH: Ensure subcortical volume in CIFTI is in LAS orientation (nipreps/niworkflows#484)
• ENH: Add option to skip brain extraction (#2039)
• ENH: Use CIFTI sampling for carpetplot when available (#2055)
• MAINT: Stop printing full boilerplate, black fmriprep/cli (#2119)
• MAINT: Ensure YAML loader is specified (#2125)
• MAINT: PIN tedana version (#2117)
• MAINT: Bump minimum Python to 3.7 (#2017)
• MAINT: Remove unused console scripts (#2048)
• MAINT: Reduce the overall size of outputs (nipreps/niworkflows#492)
• DOC: Update parallel subject neurostars link in FAQ (#2104)
• DOC: Add FAQ about reusing work directory (#2045)

20.1.0rc4

*fMRIPrep* 20.1.0 introduces a magnitude of new features and improvements.
Originally nominated to become the first LTS (long-term support) version of *fMRIPrep*, this release has been supercharged with many new features and bug-fixes.
To ensure long-term stability, we have postponed the LTS nomination to 20.2 to allow us unlocking the 20.1 earlier, and a more extensive stress testing of the series before jumping into a longer support commitment.
Some key additions in this release include:

- A centralized `configuration module
  <https://fmriprep.readthedocs.io/en/latest/api.html#module-fmriprep.config>`__
  keeping track of *fMRIPrep*'s many options and run-time and environmental
  circumstances and settings.
  The new config module, which has been also propagated to other *NiPreps*
  (`dMRIPrep <https://nipreps.org/dmriprep>`__,
  `MRIQC <https://mriqc.readthedocs.io/>`__),
  comes to robustify the run-to-run replicability of *fMRIPrep* (e.g., tracking random seeds),
  make the option handling more modular but consistent (e.g., setting the ground for a
  command-line interface built off of the config module),
  and ease troubleshooting and telemetry.
- The *anatomical preprocessing fast-track*: a new experimental command-line option
  ``--anat-derivatives <PATH>`` checks that all necessary anatomical derivatives
  required by *fMRIPrep* are present under ``<PATH>``, and skips the anatomical
  processing in full if *fMRIPrep*'s expectations are met.
  Because now functional processing of many sessions and runs can be efficiently
  split into more digestible computational units (i.e., cluster job) while guaranteeing the
  exact same anatomical results are being used, this can significantly speed up
  longitudinal study preprocessing, and it is a fundamental optimization to process
  databases of densely scanned individuals such as `My Connectome
  <https://openneuro.org/datasets/ds000031>`__.
  This option is not recommended for single-session processing.
- A change in output CIFTI2 subcortical volume orientation to be compatible with HCP Pipeline tools and data.

.. admonition:: Thanks

    With thanks to Basile Pinsard, Joe B. Wexler, Noah Benson, and Marc Bue for contributions.

.. admonition:: New Paper!

    This release comes after our latest protocol paper "*Analysis of task-based
    functional MRI data preprocessed with fMRIPrep*" has been accepted.
    The protocol describes how to use *fMRIPrep* on high-performance
    clusters to preprocess fMRI data for task-based analyses.
    Please check out `the latest version on Nature Protocols
    <https://doi.org/10.1038/s41596-020-0327-3>`__ or `the preprint
    <https://doi.org/10.1101/694364>`__.

.. 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: ``MultiLabel`` interpolations should not use ``float=True`` (#2147)
* FIX: Generate proper LTA transform prior BOLD sampling on surfaces (#2146)
* FIX: Temporary config file in work directory gets clobbered in parallel jobs (#2138)
* FIX: Dismiss ``echo`` entity on several derivatives and figures outputs (#2133)
* FIX: Correct summary report when using previously run ``recon-all`` (#2124)
* FIX: Ensure correct WM and CSF masks are picked in confounds workflow (#2128)
* FIX: Explicitly add default ``native`` resolution to volumetric outputs (`nipreps/niworkflows#494`_)
* ENH: Finish the upstreaming of *NiTransforms* interfaces to *NiWorkflows* (#2132)
* ENH: Enable filtering for ``ANY`` or ``NONE`` in ``--bids-filter-file`` (#2123)
* ENH: Use new ``DerivativesDataSink`` from *NiWorkflows* 1.2.0 (#2114)
* ENH: Config module (#2018)
* ENH: Add option to ignore T2w / FLAIR images (#2015)
* ENH: Ensure subcortical volume in CIFTI is in LAS orientation (`nipreps/niworkflows#484`_)
* ENH: Add option to skip brain extraction (#2039)
* ENH: Use CIFTI sampling for carpetplot when available (#2055)
* MAINT: Stop printing full boilerplate, ``black fmriprep/cli`` (#2119)
* MAINT: Ensure YAML loader is specified (#2125)
* MAINT: PIN *tedana* version (#2117)
* MAINT: Bump minimum Python to 3.7 (#2017)
* MAINT: Remove unused console scripts (#2048)
* MAINT: Reduce the overall size of outputs (`nipreps/niworkflows#492`_)
* DOC: Update parallel subject neurostars link in FAQ (#2104)
* DOC: Add FAQ about reusing work directory (#2045)

.. _`nipreps/niworkflows#484`: https://github.com/nipreps/niworkflows/pull/484
.. _`nipreps/niworkflows#494`: https://github.com/nipreps/niworkflows/pull/494
.. _`nipreps/niworkflows#492`: https://github.com/nipreps/niworkflows/pull/492