Merge branch 'gh-pages' into bep_dates

_bep_collection/bep041.md

@@ -0,0 +1,4 @@
+---
+redirect_to:
+  - https://docs.google.com/document/d/1KHzp-yk8KXvkUIhtN71WU0m4P4kKT9C1yvI-i9_kNeY/edit?usp=sharing
+---

_data/beps.yml

@@ -384,3 +384,15 @@
   google_doc_created: 2023-03
   pull_request_created:
   pull_request_merged:
+
+- number: "041"
+  title: Statistical Model Derivatives
+  leads:
+    - name: "[Taylor Salo](mailto:[email protected])"
+  update: New BEP, collecting community comments and feedback. All collaborators are welcome.
+  content:
+    - derivative
+  blocking: None
+  google_doc_created: 2022-08
+  pull_request_created:
+  pull_request_merged:

_data/other_converters.yml

@@ -42,8 +42,7 @@
         - PAR/REC
       expected_input:
       language:
-        C++ (compiled versions available from <a
-        href="https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage">NITRC</a>)
+        - C++ (compiled versions available from <ahref="https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage">NITRC</a>)
       comment: "dcm2nii DICOM to NIfTI converter"
 
 

_pages/index.md

@@ -4,9 +4,9 @@ layout: index
 
 # About BIDS
 
-Neuroimaging experiments result in complicated data that can be arranged in many different ways.
-So far there is no consensus how to organize and share data obtained in neuroimaging experiments.
-Even two researchers working in the same lab can opt to arrange their data in a different way.
+Neuroimaging experiments 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 data obtained in neuroimaging experiments.
+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 neuroimaging and behavioral data.
 
@@ -24,28 +24,27 @@ BIDS is developed by the community for the community and everybody can [become a
 
 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-validator](https://github.com/bids-standard/bids-validator){:target="_blank"}, to automatically check datasets for adherence to the specification, [OpenNeuro](https://openneuro.org/){:target="_blank"}, as a database for BIDS formatted datasets, and [BIDS-Apps](https://doi.org/10.1371/journal.pcbi.1005209){:target="_blank"}, a collection of portable neuroimaging pipelines that understand BIDS datasets.
+A few of the key elements of this ecosystem are the [BIDS specification](http://bids-specification.readthedocs.io/) with the nitty-gritty details, the [BIDS starter kit](https://bids-standard.github.io/bids-starter-kit/) with a simple explanation how to work with it, the [BIDS validator](https://github.com/bids-standard/bids-validator){:target="_blank"} to automatically check datasets for adherence to the specification, [BIDS Apps](https://doi.org/10.1371/journal.pcbi.1005209){:target="_blank"}, a collection of portable neuroimaging pipelines that understand BIDS datasets, and [OpenNeuro](https://openneuro.org/){:target="_blank"}, as a database for BIDS formatted datasets.
 
 A non-exhaustive list of further tools can be found in the [Benefits](https://bids.neuroimaging.io/benefits.html) section.
 
-With the ongoing development of new tools and resources it is important to keep in mind that the BIDS specification remains the standard according to which the entire ecosystem must adhere.
+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.
 
 ## Further Information
 
-- Good introductions to the BIDS standard can be found in the initial [paper published in Nature Scientific Data](https://www.nature.com/articles/sdata201644){:target="_blank"}, as well as in the follow up papers on specific modalities: [MEG](https://www.nature.com/articles/sdata2018110){:target="_blank"}, [EEG](https://www.nature.com/articles/s41597-019-0104-8){:target="_blank"}, and [iEEG](https://www.nature.com/articles/s41597-019-0105-7){:target="_blank"}.
+- Good introductions to the BIDS standard can be found in the initial [paper published in Nature Scientific Data](https://www.nature.com/articles/sdata201644){:target="_blank"}, as well as in the follow up papers on specific modalities: [MEG](https://www.nature.com/articles/sdata2018110){:target="_blank"}, [EEG](https://www.nature.com/articles/s41597-019-0104-8){:target="_blank"}, [iEEG](https://www.nature.com/articles/s41597-019-0105-7){:target="_blank"}, [genetics](https://doi.org/10.1093/gigascience/giaa104){:target="_blank"}, [PET](https://doi.org/10.1038/s41597-022-01164-1){:target="_blank"}, [microscopy](https://doi.org/10.3389/fnins.2022.871228){:target="_blank"}, and [qMRI](https://doi.org/10.1038/s41597-022-01571-4){:target="_blank"}.
 
 - Look through some of the community's [presentations on BIDS](https://osf.io/yn93h/){:target="_blank"}.
 
-- We have constructed a [grant writing kit](https://docs.google.com/document/d/1Q7JTOvUqt05YQfnbvGoP1SZQy_CGkNEVcsVZeS4D5_o/edit){:target="_blank"} to assist grant writers putting together BIDS related grant proposals.
-
 - Take a look at how the community [uses BIDS](https://medium.com/stanford-center-for-reproducible-neuroscience/bids-usage-survey-results-72637ff039c4){:target="_blank"}.
 
+- We have constructed a [grant writing kit](https://docs.google.com/document/d/1Q7JTOvUqt05YQfnbvGoP1SZQy_CGkNEVcsVZeS4D5_o/edit){:target="_blank"} 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){:target="_blank"}. Please find our [associated application](./BIDS-materials/2020_TheNeuro_OpenScienceInAction_application.pdf){:target="_blank"}.
 
 ## Communication channels
 
-If you are interested in receiving occasional updates around BIDS,
-feel free to join one of the communication channels that we use regularly:
+If you are interested in receiving occasional updates around BIDS, feel free to join one of the communication channels that we use regularly:
 
 - The `bids-discussions` Google Group for [updates via email](https://groups.google.com/g/bids-discussion){:target="_blank"}
 - Follow BIDS on [Twitter](https://twitter.com/BIDSstandard?ref_src=twsrc%5Etfw){:target="_blank"}