[doc] list templateflow templates that need to be prefetched for fmriprep i… #2196

bpinsard · 2020-06-21T01:30:21Z

…nternal usage

Changes proposed in this pull request

Improve documentation to fix #2195
Some templateflow templates are required by fmriprep independent of requested output-spaces.
In the case were it needs to be prefetched, these need to be prefetched as well.

Documentation that should be reviewed

faq.rst

…nternal usage

mgxd · 2020-06-22T13:13:58Z

docs/faq.rst

+In addition to the output-spaces that you specify, fmriprep will use
+'MNI152NLin2009cAsym', 'MNI152NLin6Asym' and 'OASIS30ANTs' templates, that


I'm fairly sure MNI152NLin6Asym is only required if aroma or cifti outputs are specified.

Suggested change

In addition to the output-spaces that you specify, fmriprep will use

'MNI152NLin2009cAsym', 'MNI152NLin6Asym' and 'OASIS30ANTs' templates, that

In addition to the output-spaces that you specify, *fMRIPrep* will use

``MNI152NLin2009cAsym``, ``MNI152NLin6Asym`` and ``OASIS30ANTs`` templates, that

mgxd · 2020-06-23T20:48:56Z

this looks good, could you update the styling as mentioned in #2196 (comment)?

docs/faq.rst

bpinsard

apply suggested changes

Co-authored-by: Oscar Esteban <[email protected]>

…/fmriprep into doc/templates_required_internal

oesteban · 2020-06-28T05:29:58Z

docs/faq.rst

+If the ``--skull-strip-template`` option is not set, then ``OASIS30ANTs``
+will be used.
+Finally, either ``--cifti-output`` or ``--use-aroma`` arguments require ``MNI152NLin6Asym``,
+that also need to be prefetched.


Suggested change

that also need to be prefetched.

that also needs to be prefetched.

mgxd

Minor rewording. The unrelated failing builds should be fixed now

docs/faq.rst

Co-authored-by: Mathias Goncalves <[email protected]>

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)

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

list templateflow templates that need to be prefetched for fmriprep i…

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…nternal usage

mgxd reviewed Jun 22, 2020

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specify internal templates depending on execution options

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reformatting

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oesteban reviewed Jun 24, 2020

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bpinsard commented Jun 25, 2020

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bpinsard and others added 3 commits June 25, 2020 09:11

Apply suggestions from code review

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Co-authored-by: Oscar Esteban <[email protected]>

fix typos

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Merge branch 'doc/templates_required_internal' of github.com:bpinsard…

904478e

…/fmriprep into doc/templates_required_internal

oesteban reviewed Jun 28, 2020

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mgxd approved these changes Jul 1, 2020

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Update docs/faq.rst

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Co-authored-by: Mathias Goncalves <[email protected]>

mgxd merged commit 3b1dabd into nipreps:master Jul 7, 2020

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[doc] list templateflow templates that need to be prefetched for fmriprep i… #2196

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		In addition to the output-spaces that you specify, fmriprep will use
		'MNI152NLin2009cAsym', 'MNI152NLin6Asym' and 'OASIS30ANTs' templates, that

	that also need to be prefetched.
	that also needs to be prefetched.

[doc] list templateflow templates that need to be prefetched for fmriprep i… #2196

[doc] list templateflow templates that need to be prefetched for fmriprep i… #2196

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bpinsard commented Jun 21, 2020

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