Landing page

.gitignore

@@ -7,6 +7,7 @@ docs/extensions/beps
 # ignore for now files that are copied from the bids examples and spe
 docs/examples/
 docs/extensions/macros_doc.md
+docs/assets/img/logos/BIDS_logo_black.svg
 
 # folders
 *.DS_Store

.pre-commit-config.yaml

@@ -47,6 +47,36 @@ repos:
     -   id: pretty-format-toml
         args: [--autofix, --indent, '4', --no-sort, --trailing-commas]
 
+-   repo: https://github.com/djlint/djLint
+    rev: v1.36.4
+    hooks:
+    -   id: djlint
+        exclude: |
+            (?x)^(
+                docs/overrides/main.html|
+                docs/overrides/404.html
+            )$
+    -   id: djlint-reformat
+        exclude: |
+            (?x)^(
+                docs/overrides/main.html|
+                docs/overrides/404.html
+            )$
+    -   id: djlint-jinja
+        exclude: |
+            (?x)^(
+                docs/overrides/main.html|
+                docs/overrides/404.html|
+                templates/.*
+            )$
+    -   id: djlint-reformat-jinja
+        exclude: |
+            (?x)^(
+                docs/overrides/main.html|
+                docs/overrides/404.html|
+                templates/.*
+            )$
+
 -   repo: https://github.com/psf/black-pre-commit-mirror
     rev: 25.11.0
     hooks:

Makefile

@@ -15,6 +15,7 @@ update_from_spec:
 	rm -fr docs/specification
 	mkdir -p docs/specification/
 	cp specification/macros_doc.md docs/extensions/macros_doc.md
+	cp -f specification/BIDS_logo/BIDS_logo_black.svg docs/assets/img/logos/
 
 update_contributors: .venv node_modules
 	@echo "  ----------------------------------  "

docs/index.md

@@ -1,165 +1,4 @@
 ---
+template: home.html
 title: BIDS
 ---
-
-Experiments in neuroscience result in complex data that can be arranged in many different ways.
-For a long time, there was no consensus how to organize and share experimental data.
-Even two researchers working in the same lab could opt to arrange their data in a different way.
-Lack of consensus (or a standard) leads to misunderstandings and time wasted on rearranging data
-or rewriting scripts expecting certain structure.
-With the Brain  Imaging Data Structure (BIDS),
-we describe a simple and easy to adopt way of organizing neural and associated, such as behavioral, data.
-
-![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 is a community effort
-
-BIDS is developed by the community for the community
-and everybody can [become a part of the community](./extensions/index.md).
-
-The most important part of BIDS are the users:
-if more people use it, more data will be shared and the more powerful it will become.
-
-<strong>We want to make it easy to learn</strong> and more adopted.
-
-Since BIDS is platform independent
-and still an adapting, growing tool, the greater the community, the better it will be.
-
-## Specification vs. Ecosystem
-
-Since the inception of the BIDS specification that documents how to organize neural and associated 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 [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 pipelines that understand BIDS datasets,
-and [OpenNeuro][openneuro] as a database for BIDS formatted 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
-
-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)
-
-## Benefits
-
-<div class="grid cards" markdown>
-
--   :material-account-group:{ .lg .middle } **For the public good**
-
-    ---
-
-    -   Lowers scientific waste
-    -   Gives opportunity to less-funded researchers
-    -   Improves efficiency
-    -   Spurs innovation
-
--   :recycle:{ .lg .middle } **For yourself**
-
-    ---
-
-    -   You are likely the future user of the data and data analysis pipelines you’ve developed
-
-    -   Enables and simplifies collaboration
-
-    -   Reviewers and funding agencies like to see reproducible results
-
-    -   Open-science based funding opportunities and awards available
-        (for instance: OHBM Replication Award, Mozilla Open Science Fellowship,
-        Google Summer of Code, and so on.)
-
-</div>
-
-By using this standard you will benefit in the following ways:
-
--   It will be easy for another researcher to work on your data.
-    To understand the organization of the files and their format you will only need to refer them to this document.
-    This is especially important if you are running your own lab and anticipate more than one person working on the same data over time.
-    By using BIDS you will save time trying to understand and reuse data acquired by a graduate student or postdoc that has already left the lab.
-
--   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.
-    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.
-
-## Further information
-
--   Good introductions to the BIDS standard can be found in the initial
-   [paper published in 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),
-   [qMRI](https://doi.org/10.1038/s41597-022-01571-4),
-   [ASL](https://www.nature.com/articles/s41597-022-01615-9),
-   [NIRS](https://www.nature.com/articles/s41597-024-04136-9),
-   [motion](https://www.nature.com/articles/s41597-024-03559-8),
-   and [MRS](https://www.nature.com/articles/s41597-025-05543-2).
-
--   Look through some of the community's [presentations on BIDS](https://osf.io/yn93h/).
-
--   Take a look at how the community [uses BIDS](https://medium.com/stanford-center-for-reproducible-neuroscience/bids-usage-survey-results-72637ff039c4).
-
--   We have constructed a [grant writing kit](./impact/index.md)
-    to assist you in putting together BIDS-related grant proposals.
-
--   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).
-
-**Leave comments about the site below:**
-
----
-
-<div style="display: flex; justify-content: space-evenly; align-items: center; flex-wrap: wrap">
-  <div>
-    <a href="https://www.incf.org/">
-      <img src="./assets/img/logos/INCF.png"
-           alt="INCF"
-           width=200px>
-    </a>
-  </div>
-  <div>
-    <a href="https://summerofcode.withgoogle.com/">
-      <img src="./assets/img/logos/GSoC_220px.png"
-           alt="GSOC"
-           width=200px>
-    </a>
-  </div>
-  <div>
-    <a href="http://grantome.com/grant/NIH/R24-MH114705-01">
-      <img src="./assets/img/logos/NIH.png"
-           alt="NIH"
-            width=200px>
-    </a>
-  </div>
-  <div>
-    <a href="https://www.arnoldventures.org/newsroom/laura-and-john-arnold-foundation-announces-3-8-million-grant-to-stanford-university-to-improve-the-quality-of-neuroscience-research">
-      <img src="./assets/img/logos/arnold_foundation.png"
-           alt="Arnold Ventures"
-           width=200px>
-    </a>
-  </div>
-</div>