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It also permits to quickly see how out-of-date someone's version is.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