[doc] update reference in "Refinement of Brain Mask" description #2215
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effigies
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Co-authored-by: Chris Markiewicz <effigies@gmail.com>
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20.2.0 RC0 (September 04, 2020) 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! A full list of changes can be found below. * FIX: Revise the reproducibility of CompCor masks (nipreps#2130) * FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239) * FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201) * FIX: Storing ``--bids-filters`` within config file (nipreps#2177) * FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803) * FIX: FreeSurfer license manipulation & canary * ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248) * ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223) * ENH: Reuse config (nipreps#2240) * ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233) * ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203) * ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204) * ENH: Report number of echoes in BOLD summary. (nipreps#2184) * ENH: Ensure NiPype telemetry is just pinged once (nipreps#2168) * DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215) * DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196) * DOC: Update references to https://github.com/nipreps (nipreps#2191) * DOC: Pin NiPype with new Sphinx extension syntax (nipreps#2092) * MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253) * MAINT: Silence PyBIDS warning by setting extension mode (nipreps#2250) * MAINT: Drop CircleCI docs build (nipreps#2247) * MAINT: Pin latest *NiPreps* (nipreps#2244) * MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183) * MAINT: Delete release-drafter (nipreps#2169) * MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165) * MAINT: Remove auto-comment bot (nipreps#2166) * MAINT: Improve the questions on the bug-report template (nipreps#2158)
HippocampusGirl
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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 (nipreps#2271)
* FIX: Restore ``--ignore t2w/flair`` options (nipreps#2260)
* FIX: Revise the reproducibility of *CompCor* masks (nipreps#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201)
* FIX: Storing ``--bids-filters`` within config file (nipreps#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803)
* FIX: *FreeSurfer* license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223)
* ENH: Reuse config (nipreps#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204)
* ENH: Report number of echoes in BOLD summary. (nipreps#2184)
* ENH: Ensure *NiPype* telemetry is just pinged once (nipreps#2168)
* DOC: Add FAQ entry for using pre-indexed layouts (nipreps#2256)
* DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196)
* DOC: Update references to https://github.com/nipreps (nipreps#2191)
* DOC: Pin *NiPype* with new Sphinx extension syntax (nipreps#2092)
* MAINT: Track nipreps#2269 and nipreps#2269, bug-fixes on the 20.1.x series
* MAINT: Remove derivatives from layout index ignores (nipreps#2258)
* MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253)
* MAINT: Silence *PyBIDS* warning by setting extension mode (nipreps#2250)
* MAINT: Drop CircleCI docs build (nipreps#2247)
* MAINT: Pin latest *NiPreps* (nipreps#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183)
* MAINT: Delete release-drafter (nipreps#2169)
* MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165)
* MAINT: Remove auto-comment bot (nipreps#2166)
* MAINT: Improve the questions on the bug-report template (nipreps#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
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Changes proposed in this pull request
Closes #2214.
grow_maskto new niworkflows interfaceRefineBrainMask.Documentation that should be reviewed
The
Refinement of Brain Masksection in workflows.rst.