20.1.1 (June 04, 2020)

======================
Bug-fix release in the 20.1.x series.

* FIX: FreeSurfer license manipulation & canary (nipreps#2165)
* FIX: Dismiss ``echo`` entity from SDC reports (nipreps#2160)
* FIX: Ensure the command-line alias of ``--nprocs`` is respected (nipreps#2152)
* MAINT: Use legacy pip/setuptools for py2 checking (nipreps#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
  <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
  <https://fmriprep.readthedocs.io/en/latest/usage.html#the-anatomical-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.

CHANGES
-------

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

.. _`nipreps/niworkflows#484`: nipreps/niworkflows#484
.. _`nipreps/niworkflows#494`: nipreps/niworkflows#494
.. _`nipreps/niworkflows#492`: nipreps/niworkflows#492

.. admonition:: Author list for papers based on *fMRIPrep* v20.1.x series

    As described in the `Contributor Guidelines
    <https://github.com/poldracklab/fmriprep/blob/e3d3bc51dbf03215e3e4d2746d8aaacdd9afb84d/CONTRIBUTING.md#publications>`__, anyone
    listed as developer or contributor may write and submit manuscripts regarding
    *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`\ ; Ciric, Rastko \ :sup:`1`\ ; Salo, Taylor \ :sup:`4`\ ; de la Vega, Alejandro \ :sup:`5`\ ; Finc, Karolina \ :sup:`6`\ ; Feingold, Franklin \ :sup:`1`\ ; Tooley, Ursula A. \ :sup:`7`\ ; Benson, Noah C. \ :sup:`8`\ ; Urchs, Sebastian \ :sup:`2`\ ; Blair, Ross W. \ :sup:`1`\ ; Erramuzpe, Asier \ :sup:`9`\ ; Lurie, Daniel J. \ :sup:`10`\ ; Basile Pinsard \ :sup:`11`\ ; Heinsfeld, Anibal S. \ :sup:`12`\ ; Jacoby, Nir \ :sup:`13`\ ; Frederick, Blaise B. \ :sup:`14, 15`\ ; Valabregue, Romain \ :sup:`16`\ ; Sneve, Markus H. \ :sup:`17`\ ; Liem, Franz \ :sup:`18`\ ; Adebimpe, Azeez \ :sup:`19`\ ; Velasco, Pablo \ :sup:`20`\ ; Wexler, Joseph B. \ :sup:`1`\ ; Groen, Iris I. A. \ :sup:`21`\ ; Ma, Feilong \ :sup:`22`\ ; Rivera-Dompenciel, Adriana \ :sup:`3`\ ; Amlien, Inge K. \ :sup:`17`\ ; Cieslak, Matthew \ :sup:`19`\ ; Devenyi, Grabriel A. \ :sup:`23`\ ; Ghosh, Satrajit S. \ :sup:`24, 25`\ ; Gomez, Daniel E. P. \ :sup:`26`\ ; Halchenko, Yaroslav O. \ :sup:`22`\ ; Isik, Ayse Ilkay \ :sup:`27`\ ; Moodie, Craig A. \ :sup:`1`\ ; Naveau, Mikaël \ :sup:`28`\ ; Satterthwaite, Theodore D. \ :sup:`19`\ ; Sitek, Kevin R. \ :sup:`29`\ ; Stojić, Hrvoje \ :sup:`30`\ ; Thompson, William H. \ :sup:`1`\ ; Wright, Jessey \ :sup:`1`\ ; Ye, Zhifang \ :sup:`31`\ ; Gorgolewski, Krzysztof J. \ :sup:`1`\ ; Poldrack, Russell A. \ :sup:`1`\ ; Esteban, Oscar \ :sup:`1`\ .

    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. University of Texas at Austin
      6. Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń
      7. Department of Neuroscience, University of Pennsylvania, PA, USA
      8. Department of Psychology, New York University
      9. Computational Neuroimaging Lab, BioCruces Health Research Institute
      10. Department of Psychology, Columbia University
      11. Department of Psychology, University of California, Berkeley
      12. SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada
      13. Child Mind Institute
      14. 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
      15. McLean Hospital Brain Imaging Center, MA, USA
      16. Consolidated Department of Psychiatry, Harvard Medical School, MA, USA
      17. Center for Lifespan Changes in Brain and Cognition, University of Oslo
      18. URPP Dynamics of Healthy Aging, University of Zurich
      19. Perelman School of Medicine, University of Pennsylvania, PA, USA
      20. Center for Brain Imaging, New York University
      21. Department of Psychology, New York University, NY, USA
      22. Dartmouth College: Hanover, NH, United States
      23. Department of Psychiatry, McGill University
      24. McGovern Institute for Brain Research, MIT, MA, USA
      25. Department of Otolaryngology, Harvard Medical School, MA, USA
      26. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen
      27. Max Planck Institute for Empirical Aesthetics
      28. Cyceron, UMS 3408 (CNRS - UCBN), France
      29. Speech & Hearing Bioscience & Technology Program, Harvard University
      30. Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London
      31. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University

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`` (nipreps#2147)
* FIX: Generate proper LTA transform prior BOLD sampling on surfaces (nipreps#2146)
* FIX: Temporary config file in work directory gets clobbered in parallel jobs (nipreps#2138)
* FIX: Dismiss ``echo`` entity on several derivatives and figures outputs (nipreps#2133)
* FIX: Correct summary report when using previously run ``recon-all`` (nipreps#2124)
* FIX: Ensure correct WM and CSF masks are picked in confounds workflow (nipreps#2128)
* FIX: Explicitly add default ``native`` resolution to volumetric outputs (`nipreps/niworkflows#494`_)
* ENH: Finish the upstreaming of *NiTransforms* interfaces to *NiWorkflows* (nipreps#2132)
* ENH: Enable filtering for ``ANY`` or ``NONE`` in ``--bids-filter-file`` (nipreps#2123)
* ENH: Use new ``DerivativesDataSink`` from *NiWorkflows* 1.2.0 (nipreps#2114)
* ENH: Config module (nipreps#2018)
* ENH: Add option to ignore T2w / FLAIR images (nipreps#2015)
* ENH: Ensure subcortical volume in CIFTI is in LAS orientation (`nipreps/niworkflows#484`_)
* ENH: Add option to skip brain extraction (nipreps#2039)
* ENH: Use CIFTI sampling for carpetplot when available (nipreps#2055)
* MAINT: Stop printing full boilerplate, ``black fmriprep/cli`` (nipreps#2119)
* MAINT: Ensure YAML loader is specified (nipreps#2125)
* MAINT: PIN *tedana* version (nipreps#2117)
* MAINT: Bump minimum Python to 3.7 (nipreps#2017)
* MAINT: Remove unused console scripts (nipreps#2048)
* MAINT: Reduce the overall size of outputs (`nipreps/niworkflows#492`_)
* DOC: Update parallel subject neurostars link in FAQ (nipreps#2104)
* DOC: Add FAQ about reusing work directory (nipreps#2045)

.. _`nipreps/niworkflows#484`: nipreps/niworkflows#484
.. _`nipreps/niworkflows#494`: nipreps/niworkflows#494
.. _`nipreps/niworkflows#492`: nipreps/niworkflows#492

20.1.0rc3

*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 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>`__.
- 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: Temporary config file in work directory gets clobbered in parallel jobs (nipreps#2138)
* FIX: Dismiss ``echo`` entity on several derivatives and figures outputs (nipreps#2133)
* FIX: Correct summary report when using previously run ``recon-all`` (nipreps#2124)
* FIX: Ensure correct WM and CSF masks are picked in confounds workflow (nipreps#2128)
* FIX: Explicitly add default ``native`` resolution to volumetric outputs (`nipreps/niworkflows#494`_)
* ENH: Finish the upstreaming of *NiTransforms* interfaces to *NiWorkflows* (nipreps#2132)
* ENH: Enable filtering for ``ANY`` or ``NONE`` in ``--bids-filter-file`` (nipreps#2123)
* ENH: Use new ``DerivativesDataSink`` from *NiWorkflows* 1.2.0 (nipreps#2114)
* ENH: Config module (nipreps#2018)
* ENH: Add option to ignore T2w / FLAIR images (nipreps#2015)
* ENH: Ensure subcortical volume in CIFTI is in LAS orientation (`nipreps/niworkflows#484`_)
* ENH: Add option to skip brain extraction (nipreps#2039)
* ENH: Use CIFTI sampling for carpetplot when available (nipreps#2055)
* MAINT: Stop printing full boilerplate, ``black fmriprep/cli`` (nipreps#2119)
* MAINT: Ensure YAML loader is specified (nipreps#2125)
* MAINT: PIN *tedana* version (nipreps#2117)
* MAINT: Bump minimum Python to 3.7 (nipreps#2017)
* MAINT: Remove unused console scripts (nipreps#2048)
* MAINT: Reduce the overall size of outputs (`nipreps/niworkflows#492`_)
* DOC: Update parallel subject neurostars link in FAQ (nipreps#2104)
* DOC: Add FAQ about reusing work directory (nipreps#2045)

.. _`nipreps/niworkflows#484`: nipreps/niworkflows#484
.. _`nipreps/niworkflows#494`: nipreps/niworkflows#494
.. _`nipreps/niworkflows#492`: nipreps/niworkflows#492

20.0.7 (May 5, 2020)

====================
Bug-fix release in the 20.0.x series.

This release includes a new, portable version of the templateflow python client. This includes an
automatic check to fetch the latest templateflow templates every time.

  * MAINT: Bump templateflow to auto-update template skeleton

20.0.6 (April 16, 2020)

Bug-fix release in the 20.0.x series.

This release fixes a bug for **phase-difference fieldmaps that are not in RAS+ orientation**.
The bug presented as an error if the orientation was reordered relative to RAS+ (for example,
AIL+) and the swapped dimensions were not of the same size.
Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle
if the original orientation was LAS+.
Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not
currently considered problematic.

This bug affects all earlier versions of fMRIPrep, except for 1.5.10 and any future releases in
the 1.5.x series.

* FIX: Do not reorient magnitude images nipreps/sdcflows#98

1.5.10 (April 16, 2020)

Bug-fix release in the 1.5.x series.

This release fixes a bug for **phase-difference fieldmaps that are not in RAS+ orientation**.
The bug presented as an error if the orientation was reordered relative to RAS+ (for example,
AIL+) and the swapped dimensions were not of the same size.
Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle
if the original orientation was LAS+.
Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not
currently considered problematic.

This bug affects all previous versions of fMRIPrep, as well as versions 20.0.0-20.0.5.

* FIX: Do not reorient magnitude images (nipreps/sdcflows#98)

20.1.0rc2 (April 9, 2020)

=========================
The second release candidate of the *fMRIPrep* 20.1.x series. This release fixes numerous issues, as well as improves carpetplot visualizations when CIFTI output is used and reduces overall output size by downcasting the datatype precision of certain outputs.

  * ENH: Use CIFTI for carpetplot when available (nipreps#2055)
  * FIX: Explicitly add default native resolution to volumetric outputs (`nipreps/niworkflows#494`_)
  * MAINT: Remove unused console scripts (nipreps#2048)
  * MAINT: Reduce overall size of outputs (`nipreps/niworkflows#492`_)

.. _`nipreps/niworkflows#494`: nipreps/niworkflows#494
.. _`nipreps/niworkflows#492`: nipreps/niworkflows#492

20.1.0rc1 (March 23, 2020)

==========================
The first release candidate of the *fMRIPrep* 20.1.x series. This release introduces a configuration
file to easily distinguish which options were selected for each participant, along with other enhancements.

  * DOC: Add FAQ about reusing work directory (nipreps#2045)
  * ENH: Config module (nipreps#2018)
  * ENH: Add option to ignore T2w / FLAIR images (nipreps#2015)
  * ENH: Ensure subcortical volume in CIFTI is in LAS orientation (`nipreps/niworkflows#484`_)
  * ENH: Add option to skip brain extraction (nipreps#2039)
  * MAINT: Bump minimum Python to 3.7 (nipreps#2017)

.. _`nipreps/niworkflows#484`: nipreps/niworkflows#484

20.0.5 (March 19, 2020)

Bug-fix release in 20.0.x series.

With thanks to James Kent for the fix and Blaise Frederick for the report and testing.

* FIX: Add CE agent to output figure filename templates (nipreps/niworkflows#482)