Merge pull request #2474 from nipreps/docs/boilerplate-to-nipreps

DOC: Refactor README and citing information

.circleci/config.yml

@@ -88,7 +88,6 @@ jobs:
               echo "them to your fork with ``git push origin --tags``"
             fi
             sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/fmriprep_docker.py
-            sed -i -E "s/(var version = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" docs/citing.rst
             sed -i "s/title = {FMRIPrep}/title = {FMRIPrep ${CIRCLE_TAG:-$THISVERSION}}/" fmriprep/data/boilerplate.bib
             # Build docker image
             e=1 && for i in {1..5}; do

README.rst

@@ -1,10 +1,8 @@
 *fMRIPrep*: A Robust Preprocessing Pipeline for fMRI Data
 =========================================================
-
-This pipeline is developed by the `Poldrack lab at Stanford University
-<https://poldracklab.stanford.edu/>`_ for use at the `Center for Reproducible
-Neuroscience (CRN) <http://reproducibility.stanford.edu/>`_, as well as for
-open-source software distribution.
+*fMRIPrep* is a *NiPreps (NeuroImaging PREProcessing toolS)* application
+(`www.nipreps.org <https://www.nipreps.org>`__) for the preprocessing of
+task-based and resting-state functional MRI (fMRI).
 
 .. image:: https://img.shields.io/badge/docker-nipreps/fmriprep-brightgreen.svg?logo=docker&style=flat
   :target: https://hub.docker.com/r/nipreps/fmriprep/tags/
@@ -79,10 +77,8 @@ This tool allows you to easily do the following:
 More information and documentation can be found at
 https://fmriprep.readthedocs.io/
 
-
 Principles
 ----------
-
 *fMRIPrep* is built around three principles:
 
 1. **Robustness** - The pipeline adapts the preprocessing steps depending on
@@ -100,34 +96,53 @@ Principles
    the process and decide which subjects should be kept for the group level
    analysis.
 
-
-Limitations and reasons not to use *fMRIPrep*
----------------------------------------------
-
-1. Very narrow :abbr:`FoV (field-of-view)` images oftentimes do not contain
-   enough information for standard image registration methods to work correctly.
-   Also, problems may arise when extracting the brain from these data.
-   Supporting these particular images is already a future line of the development
-   road-map.
-2. *fMRIPrep* may also underperform for particular populations (e.g., infants) and
-   non-human brains, although appropriate templates can be provided to overcome the
-   issue.
-3. The "EPInorm" approach is currently not supported, although we plan to implement
-   this feature (see `#620 <https://github.com/nipreps/fmriprep/issues/620>`_).
-4. If you really want unlimited flexibility (which is obviously a double-edged sword).
-5. If you want students to suffer through implementing each step for didactic purposes,
-   or to learn shell-scripting or Python along the way.
-6. If you are trying to reproduce some *in-house* lab pipeline.
-
-(Reasons 4-6 were kindly provided by S. Nastase in his
-`open review <https://pubpeer.com/publications/6B3E024EAEBF2C80085FDF644C2085>`__
-of our `pre-print <https://doi.org/10.1101/306951>`__).
-
+Citation
+--------
+**Citation boilerplate**.
+Please acknowledge this work using the citation boilerplate that *fMRIPrep* includes
+in the visual report generated for every subject processed.
+For a more detailed description of the citation boilerplate and its relevance,
+please check out the
+`NiPreps documentation <https://www.nipreps.org/intro/transparency/#citation-boilerplates>`__.
+
+**Plagiarism disclaimer**.
+The boilerplate text is public domain, distributed under the
+`CC0 license <https://creativecommons.org/publicdomain/zero/1.0/>`__,
+and we recommend *fMRIPrep* users to reproduce it verbatim in their works.
+Therefore, if reviewers and/or editors raise concerns because the text is flagged by automated
+plagiarism detection, please refer them to the *NiPreps* community and/or the note to this
+effect in the `boilerplate documentation page <https://www.nipreps.org/intro/transparency/#citation-boilerplates>`__.
+
+**Papers**.
+*fMRIPrep* contributors have published two relevant papers:
+`Esteban et al. (2019) <https://doi.org/10.1038/s41592-018-0235-4>`__
+[`preprint <https://doi.org/10.1101/306951>`__], and
+`Esteban et al. (2020) <https://doi.org/10.1038/s41596-020-0327-3>`__
+[`preprint <https://doi.org/10.1101/694364>`__].
+
+**Other**.
+Other materials that have been generated over time include the
+`OHBM 2018 software demonstration <https://effigies.github.io/fmriprep-demo/>`__
+and some conference posters:
+
+* Organization for Human Brain Mapping 2018
+  (`Abstract <https://ww5.aievolution.com/hbm1801/index.cfm?do=abs.viewAbs&abs=1321>`__;
+  `PDF <https://files.aievolution.com/hbm1801/abstracts/31779/2035_Markiewicz.pdf>`__)
+
+.. image:: _static/OHBM2018-poster_thumb.png
+   :target: _static/OHBM2018-poster.png
+
+* Organization for Human Brain Mapping 2017
+  (`Abstract <https://ww5.aievolution.com/hbm1701/index.cfm?do=abs.viewAbs&abs=4111>`__;
+  `PDF <https://f1000research.com/posters/6-1129>`__)
+
+.. image:: _static/OHBM2017-poster_thumb.png
+   :target: _static/OHBM2017-poster.png
 
 Acknowledgements
 ----------------
+This work is steered and maintained by the `NiPreps Community <https://www.nipreps.org>`__.
 
-Please acknowledge this work using the citation boilerplate that *fMRIPrep* includes
-in the visual report generated for every subject processed.
-For an illustration of how the citation boilerplate generally reads, please
-check `our documentation <https://fmriprep.readthedocs.io/en/latest/citing.html>`__.
+This work was supported by the Laura and John Arnold Foundation,
+the NIH (grant NBIB R01EB020740, PI: Ghosh),
+and NIMH (R24MH114705, R24MH117179, R01MH121867, PI: Poldrack)