20.0.0 (February 24, 2020)
==========================
The major release of 2020 is here!

*fMRIPrep* is transitioning to a calendar version system
(`#1912 <https://github.com/poldracklab/fmriprep/issues/1912>`__).
The `CalVer <https://calver.org/>`__ system reflects *fMRIPrep*'s nature
as an evolving workflow and does not impose any artificial incentive for
"big-change" releases.
It also permits to quickly see how out-of-date someone's version is.
As of now, the *default* version increment is the minor release number.
Hence, when the minor release number changes the work directory of *fMRIPrep*
will presumably break.
Micro releases only include bug-fixes that can reuse exiting working directories.

The major highlight of this release entails CIFTI generation to match
:abbr:`HCP (Human Connectome Project)` *grayordinates*.
In addition, the new *fMRIPrep 20.0.0* has gone through a major overhaul in the
handling of standard spaces (spatial normalizations, fusion of prior knowledge from
corresponding atlases) and imaging outputs.
In particular, the new series almost completely implements the new
syntax for ``--output-spaces`` to describe the (non)standard spatial references
that shall be used for generating outputs
(`#1604 <https://github.com/poldracklab/fmriprep/issues/1604>`__).

This release includes contributions from Azeez Adebimpe and Basile Pinsard - very much appreciated.

  * ENH: Warn when existing output version does not match current pipeline version (#1967)
  * ENH: Add ``--clean-workdir`` argument (#1966)
  * ENH: Refactor of how spatial normalization targets and ``--output-spaces`` are maintained (#1955) (#1983)
  * ENH: Add ``--bids-filter-file`` argument for more controlled data querying (#1770)
  * FIX: Ensure subject ID is used when selecting BIDS data (#1982)
  * FIX: Display a log message when processing completes successfully (#1977)
  * DOC: Clean up surface outputs (#1993)
  * DOC: Integrate intersphinx, drop external module wrapping (#1989)
  * DOC: Improve custom template usage description (#1969)
  * MAINT: Use local docker registry (#1990)
  * MAINT: Pin connectome-workbench 1.3.2, add to documented dependencies (#1958)
  * MAINT: Pin NiBabel, NiWorkflows, sMRIPrep (#1971)
  * MAINT: CI build error fixes (#1976)

.. admonition:: Author list for papers based on *fMRIPrep* v20.0.0

    As described in the `Contributor Guidelines
    <https://github.com/poldracklab/fmriprep/blob/d65cfdd80443c5ca779680b1087d14f189e8ceb5/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. (1); DuPre, Elizabeth (2); Goncalves, Mathias (1); Kent, James D. (3); Ciric, Rastko (1); Salo, Taylor (4); de la Vega, Alejandro (5); Finc, Karolina (6); Feingold, Franklin (1); Urchs, Sebastian (2); Blair, Ross W. (1); Erramuzpe, Asier (7); Valabregue, Romain (8); Jacoby, Nir (9); Lurie, Daniel J. (10); Heinsfeld, Anibal S. (11); Halchenko, Yaroslav O. (12); Sneve, Markus H. (13); Devenyi, Grabriel A. (14); Liem, Franz (15); Gomez, Daniel E. P. (16); Adebimpe, Azeez (17); Velasco, Pablo (18); Groen, Iris I. A. (19); Ma, Feilong (12); Rivera-Dompenciel, Adriana (3); Amlien, Inge K. (13); Cieslak, Matthew (17); Ghosh, Satrajit S. (20, 21); Isik, Ayse Ilkay (22); Moodie, Craig A. (1); Naveau, Mikaël (23); Satterthwaite, Theodore D. (17); Sitek, Kevin R. (24); Stojić, Hrvoje (25); Thompson, William H (1); Tooley, Ursula A. (26); Wright, Jessey (1); Ye, Zhifang (27); Gorgolewski, Krzysztof J. (1); Poldrack, Russell A. (1); Esteban, Oscar (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. Computational Neuroimaging Lab, BioCruces Health Research Institute
      8. 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
      9. Department of Psychology, Columbia University
      10. Department of Psychology, University of California, Berkeley
      11. Child Mind Institute
      12. Dartmouth College: Hanover, NH, United States
      13. Center for Lifespan Changes in Brain and Cognition, University of Oslo
      14. Department of Psychiatry, McGill University
      15. URPP Dynamics of Healthy Aging, University of Zurich
      16. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen
      17. Perelman School of Medicine, University of Pennsylvania, PA, USA
      18. Center for Brain Imaging, New York University
      19. Department of Psychology, New York University, NY, USA
      20. McGovern Institute for Brain Research, MIT, MA, USA
      21. Department of Otolaryngology, Harvard Medical School, MA, USA
      22. Max Planck Institute for Empirical Aesthetics
      23. Cyceron, UMS 3408 (CNRS - UCBN), France
      24. Speech & Hearing Bioscience & Technology Program, Harvard University
      25. Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London
      26. Department of Neuroscience, University of Pennsylvania, PA, USA
      27. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University

20.0.0rc3

_fMRIPrep_ is transitioning to a calendar version system [#1912](https://github.com/poldracklab/fmriprep/issues/1912).
The [CalVer](https://calver.org/) system reflects _fMRIPrep_'s nature as an evolving workflow and does not impose any artificial incentive for "big-change" releases.
It also permits to quickly see how out-of-date someone's version is.
As of now, the *default* version increment is the minor release number.
Hence, when the minor release number changes the work directory of _fMRIPrep_ will presumably break.
Micro releases only include bug-fixes that can reuse exiting working directories.

The major highlight of this release entails CIFTI generation to match HCP (Human Connectome Project) _grayordinates_.
In addition, the new _fMRIPrep 20.0.0_ has gone through a major overhaul in the handling of standard spaces (spatial normalizations, fusion of prior knowledge from corresponding atlases) and imaging outputs.
In particular, the new series almost completely implements the new syntax for `--output-spaces` to describe the (non)standard spatial references that shall be used for generating outputs [#1604](https://github.com/poldracklab/fmriprep/issues/1604).

This release includes contributions from Azeez Adebimpe and Basile Pinsard - very much appreciated.

  * ENH: Warn when existing output version does not match current pipeline version (#1967)
  * ENH: Add ``--clean-workdir`` argument (#1966)
  * ENH: Refactor of how spatial normalization targets and ``--output-spaces`` are maintained (#1955) (#1983)
  * ENH: Add ``--bids-filter-file`` argument for more controlled data querying (#1770)
  * FIX: Ensure subject ID is used when selecting BIDS data (#1982)
  * FIX: Display a log message when processing completes successfully (#1977)
  * DOC: Clean up surface outputs (#1993)
  * DOC: Integrate intersphinx, drop external module wrapping (#1989)
  * DOC: Improve custom template usage description (#1969)
  * MAINT: Use local docker registry (#1990)
  * MAINT: Pin connectome-workbench 1.3.2, add to documented dependencies (#1958)
  * MAINT: Pin NiBabel, NiWorkflows, sMRIPrep (#1971)
  * MAINT: CI build error fixes (#1976)

fMRIPrep 20.0.0rc2 (February 18, 2020)
======================================

The second and last release candidate of the new major version 20.x.x series.
*fMRIPrep* is transitioning to a calendar version system
(`#1912 <https://github.com/poldracklab/fmriprep/issues/1912>`__).
The `CalVer <https://calver.org/>`__ system reflects *fMRIPrep*'s nature
as an evolving workflow and does not impose any artificial incentive for
"big-change" releases.
It also permits to quickly see how out-of-date someone's version is.
As of now, the *default* version increment is the minor release number.
Hence, when the minor release number changes the work directory of *fMRIPrep*
will presumably break.
Micro releases only include bug-fixes that can reuse exiting working directories.

The major highlight of this release entails CIFTI generation to match
:abbr:`HCP (Human Connectome Project)` *grayordinates*.
In addition, the new *fMRIPrep 20.0.0* has gone through a major overhaul in the
handling of standard spaces (spatial normalizations, fusion of prior knowledge from
corresponding atlases) and imaging outputs.
In particular, the new series almost completely implements the new
syntax for ``--output-spaces`` to describe the (non)standard spatial references
that shall be used for generating outputs
(`#1604 <https://github.com/poldracklab/fmriprep/issues/1604>`__).

This release includes contributions from Azeez Adebimpe and Basile Pinsard - very much appreciated.

  * ENH: Warn when existing output version does not match current pipeline version (#1967)
  * ENH: Add ``--clean-workdir`` argument (#1966)
  * ENH: Refactor of how spatial normalization targets and ``--output-spaces`` are maintained (#1955) (#1983)
  * ENH: Add ``--bids-filter-file`` argument for more controlled data querying (#1770)
  * FIX: Ensure subject ID is used when selecting BIDS data (#1982)
  * FIX: Display a log message when processing completes successfully (#1977)
  * DOC: Improve custom template usage description (#1969)
  * MAINT: Pin connectome-workbench 1.3.2, add to documented dependencies (#1958)
  * MAINT: Pin NiBabel, NiWorkflows, sMRIPrep (#1971)
  * MAINT: CI build error fixes (#1976)

1.5.9 (February 14, 2020)

Bug-fix release in the 1.5.x series.

This release fixes a bug for some phase maps generated by Philips. A full fix with better handling
of all phase maps will be available in an upcoming minor release (20.0 or 20.1), but this should permit
users who are processing with 1.5.x to resolve this issue in a way that does not affect phase maps
unaffected by the bug.

  * FIX: Center phase maps around central mode, avoiding FoV-related outliers (poldracklab/sdcflows#89)

1.5.8 (January 28, 2020)

Bug-fix release in the 1.5.x series.

* FIX: SyN SDC logic failing in ``--force-syn`` cases (#1951)

1.5.7 (January 23, 2020)

Bug-fix release in the 1.5.x series.

  * FIX: Calculate FoV with shape and zooms (poldracklab/smriprep#161)

1.5.6 (January 22, 2020)

Bug-fix release in the 1.5.x series.

* FIX: Include all functional runs in reports, establish consistent ordering (#1937)
* FIX: Use SyN-SDC if --use-syn-sdc and --ignore fieldmaps are used (#1942)

1.5.5 (January 14, 2019)

Bug-fix release in the 1.5.x series.

* FIX: Correctly select volumetric spaces for carpetplot (#1932) @effigies
* FIX: Constrain setuptools for Python 2.7 installs of fmriprep-docker (#1933) @effigies

fMRIPrep 1.5.3 (December 12, 2019)

The last bug fix release of the 1.5.x series.

* FIX: Do not run STC if SliceTiming metadata is set but empty (#1854) @oesteban
* FIX: Link to EPINorm issue in README (#1903) @adelavega
* FIX: Respect --dummy-scans 0 (#1908) @jdkent
* ENH: Upgrade SDCFlows to new API (1.0.0) (#1886) @oesteban
* ENH: Add --fs-subjects-dir flag (#1901) @effigies
* DOC: Improving accessibility of confounds description (#1877) @kfinc
* MAINT: Ensure data is packaged in sdist (#1902) @effigies
* MAINT: Remove deprecated command-line arguments (#1909) @mgxd

1.5.2 (December 2, 2019)

Bug-fix release in the 1.5.x series.

* FIX: Ensure data type of masked image matches T1.mgz (poldracklab/niworkflows#430) @effigies

1.5.0rc2 (August 23, 2019)

Two hallmark changes conducive to a new minor release line have been included in
version 1.5.0: the upgrade of *PyBIDS* to the 0.9 series and the split of *SDCflows*
off from *fMRIPrep* codebase.
*PyBIDS* 0.9.x has a better handling of the indexed dataset that will permit some
optimizations to *fMRIPrep*'s memory fingerprint.
*SDCflows* now are found at `poldracklab/sdcflows <https://github.com/poldracklab/sdcflows>`__,
and have been split to allow a more granular and thorough testing in collaboration
with M. Cieslak, A. Adebimpe, and T. Satterthwaite.
Some other bugfixes, improvements to the documentation and minor features are also
shipped with the new release.

* FIX: Postpone ``pandoc`` conversion of boilerplate after workflow has fully run (#1710) @oesteban
* FIX: Use MNI152NLin2009cAsym for SDC if no templates are specified (#1703) @effigies
* FIX: Correct BOLD-T1w registration description if DoF != 9 (#1701) @effigies
* ENH: Make fmriprep print defaults for arguments with help (#1735) @gdevenyi
* ENH: Add check for updates and check whether version has been flagged. (#1715) @oesteban
* ENH: Add TaskName metadata to BOLD outputs (#1714) @effigies
* REF: Separate SDCflows from fMRIPrep (#1670) @oesteban
* DOC: Update .zenodo.json (#1732) @utooley
* DOC: Add link to documentation in help of ``--output-spaces`` argument (#1722) @oesteban
* DOC: adding recon-all issue to faq (#1622) @franklin-feingold
* DOC: Add copyright waiver to boilerplate and reviewer note to docs (#1691) @effigies
* MAINT: Bump pybids and nipype dependencies (#1744) @effigies
* MAINT: Move regression tests of EPI masks over to Niworkflows (#1716) @oesteban
* MAINT: Remove old ``extensions`` entity selector for PyBIDS queries (#1707) @oesteban
* MAINT: Use PyBIDS 0.9.x via niworkflows/smriprep PRs (#1695) @effigies