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.github/PULL_REQUEST_TEMPLATE/website.md

@@ -0,0 +1,43 @@
+<!--- Until this PR is ready for review, you can include [WIP] in the title, or create a draft PR. -->
+
+
+<!---
+Below is a suggested pull request template. Feel free to add more details you feel are relevant/necessary.
+
+-->
+
+<!--
+Please indicate after the # which issue you're closing with this PR, if applicable.
+If the PR closes multiple issues, include "Closes" before each one is listed.
+You can also link to other issues if necessary, e.g. "See also #1234".
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+- Closes #
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+<!--
+Please give a brief overview of what has changed or been added in the PR.
+This can include anything specific the maintainers should be looking for when they review the PR.
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+Changes proposed in this pull request:
+-
+
+## Checklist for contributor
+
+- [ ] PR has an interpretable title with a prefix (e.g. `[BUG]`, `[DOC]`, `[ENH]`, `[MAINT]`)\
+Refer to [NumPy Development Guide](https://numpy.org/doc/stable/dev/development_workflow.html#writing-the-commit-message) for a full list
+- [ ] PR links to GitHub issue with mention `Closes #XXXX`
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Any dependent changes have been merged and published in downstream modules
+
+<!-- To be checked off by reviewers -->
+## Checklist for reviewers
+_This section is for the PR reviewer_
+
+For new features:
+- [ ] Tests have been added
+
+For bug fixes:
+- [ ] There is at least one test that would fail under the original bug conditions

docs/index.md

@@ -1,4 +1,5 @@
 ---
+template: home.html
 title: BIDS
 ---
 
@@ -14,14 +15,9 @@ we describe a simple and easy to adopt way of organizing neuroimaging and behavi
 ![BIDS-folder-organization](./assets/img/dicom-reorganization-transparent-black_1000x477.png#only-light)
 ![BIDS-folder-organization](./assets/img/dicom-reorganization-transparent-white_1000x477.png#only-dark)
 
-BIDS was heavily inspired by the format used internally by the OpenfMRI repository
-that is now known as [OpenNeuro][openneuro].
-While working on BIDS we consulted many neuroscientists to make sure it covers most common experiments,
-but at the same time is intuitive and easy to adopt.
-The specification is intentionally based on simple file formats and folder structures
-to reflect current lab practices and make it accessible to a wide range of scientists coming from different backgrounds.
+### BIDS as a community effort
 
-## BIDS is a community effort
+<!-- a large community of researchers contributed to make sure that it includes what is needed to make the data usable -->
 
 BIDS is developed by the community for the community
 and everybody can [become a part of the community](./extensions/index.md).
@@ -34,33 +30,28 @@ if more people use it, more data will be shared and the more powerful it will be
 Since BIDS is platform independent
 and still an adapting, growing tool, the greater the community, the better it will be.
 
-## Specification vs. Ecosystem
+### BIDS as an ecosystem of tools
+
+<!-- A large ecosystem of tools and datasets based on BIDS has emerged, making BIDS the foundation for much neuroimaging analysis. -->
 
 Since the inception of the BIDS specification that documents how to organize neuroimaging data,
 a large ecosystem of tools and resources has evolved around BIDS.
 
 A few of the key elements of this ecosystem are
-the [BIDS specification](http://bids-specification.readthedocs.io/) with the nitty-gritty details,
-<!-- markdown-link-check-disable -->
+the [BIDS specification][specification] with the nitty-gritty details,
 the [starter kit](./getting_started/index.md) with a simple explanation how to work with it,
-<!-- markdown-link-check-enable -->
-the [BIDS validator](https://github.com/bids-standard/bids-validator) to automatically check datasets for adherence to the specification,
-[BIDS Apps](https://doi.org/10.1371/journal.pcbi.1005209), a collection of portable neuroimaging pipelines that understand BIDS datasets,
-and [OpenNeuro][openneuro] as a database for BIDS formatted datasets.
+the [BIDS validator][bids_validator_gh] to automatically check datasets for adherence to the specification,
+[BIDS Apps](./tools/bids-apps.md), a collection of portable neuroimaging pipelines that understand BIDS datasets.
 
 A non-exhaustive list of further tools can be found in the [tools](./tools/index.md) section.
 
 With the ongoing development of new tools and resources it is important to keep in mind
-that the [BIDS specification](http://bids-specification.readthedocs.io/) remains
-the standard according to which the entire ecosystem must adhere.
-
-## Philosophy
+that the [BIDS specification][specification]
+remains the standard according to which the entire ecosystem must adhere.
 
-Another part is that BIDS is striving to not reinventing other standards and metadata ontologies but reuse them:
-
-![BIDS-minder](./assets/img/BIDS-minder.svg)
+## Why use BIDS?
 
-## Benefits
+1) Efficient data usage: The use of a common format allows data to be more easily reused by other researchers, maximizing its utility.  2) Analysis pipelines: there is a growing number of data analysis software packages (BIDS-Apps) that can automatically process data organized according to BIDS; 3) Data sharing: Use of BIDS makes sharing by major repositories (e.g. OpenNeuro) very simple, enabling rapid and effective data sharing.
 
 <div class="grid cards" markdown>
 
@@ -98,33 +89,40 @@ By using this standard you will benefit in the following ways:
 
 -   There is a growing number of [data analysis software packages](./tools/index.md) that can understand data organized according to BIDS.
 
--   Databases such as [OpenNeuro.org](http://openneuro.org), [LORIS](http://www.loris.ca), [COINS](https://coins.trendscenter.org), [XNAT](https://central.xnat.org/), [SciTran](https://scitran.github.io/), and others will accept and export datasets organized according to BIDS.
+-   Databases such as [OpenNeuro.org][openneuro], [LORIS](http://www.loris.ca), [COINS](https://coins.trendscenter.org), [XNAT](https://central.xnat.org/), [SciTran](https://scitran.github.io/), and others will accept and export datasets organized according to BIDS.
     If you ever plan to share your data publicly (nowadays some journals require this) you can speed up the curation process by using BIDS.
 
--   There are [validation tools](https://github.com/bids-standard/bids-validator) (also available [online](http://bids-standard.github.io/bids-validator/)) that can check your dataset integrity and let you easily spot missing values.
+-   There are [validation tools][bids_validator_gh] (also available [online][bids_validator]) that can check your dataset integrity and let you easily spot missing values.
 
-## Further information
+## Foundational principles
 
--   Good introductions to the BIDS standard can be found in the initial
-   [paper published in Nature Scientific Data](https://www.nature.com/articles/sdata201644),
-   as well as in the follow up papers on specific modalities:
-   [MEG](https://www.nature.com/articles/sdata2018110),
-   [EEG](https://www.nature.com/articles/s41597-019-0104-8),
-   [iEEG](https://www.nature.com/articles/s41597-019-0105-7),
-   [genetics](https://doi.org/10.1093/gigascience/giaa104),
-   [PET](https://doi.org/10.1038/s41597-022-01164-1),
-   [microscopy](https://doi.org/10.3389/fnins.2022.871228),
-   and [qMRI](https://doi.org/10.1038/s41597-022-01571-4).
+### Reuse existing standards
 
--   Look through some of the community's [presentations on BIDS](https://osf.io/yn93h/).
+BIDS strives to reuse existing standares, formats, methods and technologies
+whenever possible to minimize complexity and facilitate adoption.
+
+![BIDS-minder](./assets/img/BIDS-minder.svg)
 
--   Take a look at how the community [uses BIDS](https://medium.com/stanford-center-for-reproducible-neuroscience/bids-usage-survey-results-72637ff039c4).
+###  Tackle most common use cases
 
--   We have constructed a [grant writing kit](./impact/index.md)
-    to assist you in putting together BIDS-related grant proposals.
+BIDS aims to tackle the most commonly used neuroimaging data, derivatives, and models
+(inspired by the [Pareto principle](https://en.wikipedia.org/wiki/Pareto_principle)).
+
+### Community engagement
+
+BIDS should enable and maximize community engagement in the creation and extension of the specification,
+to ensure maximal adoption by the research community.
+
+## Further information
+
+-   Good introductions to the BIDS standard can be found in the initial BIDS paper
+    as well as in the follow up papers for BIDS extensions.
+    All of those are listed in [the BIDS specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids).
+
+-   Look through some of the community's [presentations on BIDS](https://osf.io/yn93h/).
 
--   We submitted an application to [The Neuro Open Science in action prize 2020](https://www.mcgill.ca/neuro/open-science/neuro-open-science-action-prize-2020).
-    Please find our [associated application](./assets/BIDS-materials/2020_TheNeuro_OpenScienceInAction_application.pdf).
+-   To assist you in putting together BIDS-related grant proposals,
+    check our [impact section that contains numbers and statistics about BIDS](./impact/index.md).
 
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