deployment
+on docker hub will happen automatically via Circle-ci.
-If you want your App to show on the [BIDS website](../tools/bids-apps.md), you will have to update the `data/tools/apps.yml` in the [BIDS website repository][bids_wesbite_gh].
+If you want your App to show on the [BIDS website](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html),
+you will have to update the `data/tools/apps.yml` in the
+[BIDS website repository](https://github.com/bids-standard/bids-website/tree/main).
#### When is a new image deposited to Docker Hub?
-Even though Docker image is being build on the CI server each time you push a commit to the repository it is not automatically being pushed to Docker Hub. Only if you tag a commit, push the tag to GitHub, and the tests you configured pass a new image will be deposited in Docker Hub.
+Even though Docker image is being build on the CI server each time
+you push a commit to the repository it is not automatically being pushed to Docker Hub.
+Only if you tag a commit, push the tag to GitHub,
+and the tests you configured pass a new image will be deposited in Docker Hub.
diff --git a/docs/faq/general.md b/docs/faq/general.md
index 5299aa8e..52582134 100644
--- a/docs/faq/general.md
+++ b/docs/faq/general.md
@@ -2,7 +2,9 @@
BIDS and [NWB](https://www.nwb.org/) are compatible.
-An NWB data file is an allowed format in the iEEG-BIDS data structure. This means that one subject (AAA) with a session (BBB) can have a BIDS folder with raw iEEG data in NWB format:
+An NWB data file is an allowed format in the iEEG-BIDS data structure.
+This means that one subject (AAA) with a session (BBB)
+can have a BIDS folder with raw iEEG data in NWB format:
```text
/sub-AAA/ses-BBB/ieeg/sub-AAA_ses-BBB_task-rest_ieeg.nwb
@@ -16,7 +18,9 @@ The same subject can have another session (CCC) with raw fMRI data in BIDS:
## How can I cite BIDS?
-See the specification website for the [main publications](https://bids-specification.readthedocs.io/en/latest/01-introduction.html#citing-bids) related to BIDS and its extensions.
+See the specification website for the
+[main publications](https://bids-specification.readthedocs.io/en/latest/01-introduction.html#citing-bids)
+related to BIDS and its extensions.
BIDS references are centralized in a [zotero group](https://www.zotero.org/groups/5111637/bids).
@@ -32,7 +36,8 @@ Also look at [the list of tutorials and information about conversions](../gettin
Hyperscanning is simultaneous fMRI with multiple subjects (see this [paper](https://doi.org/10.1006/nimg.2002.1150)).
-- See this [issue](https://github.com/bids-standard/bids-specification/issues/402) in the bids specification repository for typical hyperscanning data.
+- See this [issue](https://github.com/bids-standard/bids-specification/issues/402)
+ in the bids specification repository for typical hyperscanning data.
See an example below with fMRI data:
@@ -55,7 +60,8 @@ sub-04/
sub-04_ses-dyadic2_*
```
-- See this [post on neurostars](https://neurostars.org/t/bids-structure-for-longitudinal-dyadic-data/26173) for hyperscanning longitunal data.
+- See this [post on neurostars](https://neurostars.org/t/bids-structure-for-longitudinal-dyadic-data/26173)
+ for hyperscanning longitunal data.
See an example below with fMRI data:
@@ -77,17 +83,19 @@ sub-S003/
ses-2/
```
-- See this [thread on the bids discussion forum](https://groups.google.com/g/bids-discussion/c/v660DuzOf3w/m/q-0PLHt5BgAJ)
+- See this [thread on the bids discussion forum](https://groups.google.com/g/bids-discussion/c/v660DuzOf3w/m/q-0PLHt5BgAJ)
## How to import Excel files to TSV file?
See [our sections on TSV files](../getting_started/folders_and_files/metadata/tsv.md) for more information.
-See also this bids tool to import and export a `participants.tsv` file: [bids-matlab-tools](https://github.com/sccn/bids-matlab-tools/blob/master/bids_spreadsheet2participants.m)
+See also this bids tool to import and export a `participants.tsv` file:
+[bids-matlab-tools](https://github.com/sccn/bids-matlab-tools/blob/master/bids_spreadsheet2participants.m)
## How to specify the micro sign in MATLAB?
-BIDS requires physical units to be specified according to the SI unit symbol and possibly prefix symbol (for example: mV, μV for milliVolt and microVolt).
+BIDS requires physical units to be specified according to the SI unit symbol and
+possibly prefix symbol (for example: mV, μV for milliVolt and microVolt).
The symbol used to indicate `µ` has unicode U+00B5, which is in MATLAB:
@@ -103,45 +111,74 @@ native2unicode(181, 'latin1')
## I had to split the testing of one of my participants across 2 days, should I use 2 different session folders to organize the data of that participant?
-No. The `session` level in the BIDS folder hierarchy can be used to group data that go "logically" together: this means that you can put in the same `session` folder data that were acquired on different days, but that are "linked" to one another in a way that make sense to how you want to organize your data.
+No. The `session` level in the BIDS folder hierarchy can be used to group data
+that go "logically" together: this means that you can put in the same `session` folder
+data that were acquired on different days,
+but that are "linked" to one another in a way that make sense to how you want to organize your data.
-If you want to keep track of what data was acquired when you can use the [`scans.tsv` files](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file).
+If you want to keep track of what data was acquired when you can use the
+[`scans.tsv` files](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file).
-For some examples, see this [issue in the bids-starter kit](https://github.com/bids-standard/bids-starter-kit/issues/193).
+For some examples, see this
+[issue in the bids-starter kit](https://github.com/bids-standard/bids-starter-kit/issues/193).
-If you deal with EEG data, you may want to read this [comment in another issue](https://github.com/bids-standard/bids-starter-kit/issues/265#issuecomment-1082240834) as well before considering combining recordings acquired on different occasions within the same `session` folder.
+If you deal with EEG data, you may want to read this
+[comment in another issue](https://github.com/bids-standard/bids-starter-kit/issues/265#issuecomment-1082240834)
+as well before considering combining recordings acquired on different occasions
+within the same `session` folder.
## Is there a machine readable version of the BIDS specification?
-Yes. The BIDS specification exist as a schema. The BIDS schema is a machine readable representation of the BIDS Standard. It is (by and large) the BIDS Specification, but written in a declarative form.
+Yes. The BIDS specification exist as a schema.
+The BIDS schema is a machine readable representation of the BIDS Standard.
+It is (by and large) the BIDS Specification, but written in a declarative form.
The BIDS schema is available in two machine readable formats:
-- as a set of [YAML](https://en.wikipedia.org/wiki/YAML) files in the [BIDS specification repository](https://github.com/bids-standard/bids-specification/tree/master/src/schema)
-- as a [single json file](https://bids-specification.readthedocs.io/en/stable/schema.json)
+- as a set of [YAML](https://en.wikipedia.org/wiki/YAML) files in the [BIDS specification repository](https://github.com/bids-standard/bids-specification/tree/master/src/schema)
+- as a [single json file](https://bids-specification.readthedocs.io/en/stable/schema.json)
-A light-weight introduction to the schema can be found [here](../standards/schema/index.md).
+A light-weight introduction to the schema can be found [here](https://bids-extensions.readthedocs.io/en/latest/schema/).
-A full description of the schema can be found on this [website](https://bidsschematools.readthedocs.io/en/latest/?badge=latest) where you will also find the documentation for the python package to interact with the schema, [bidsschematools](https://pypi.org/project/bidsschematools/).
+A full description of the schema can be found on this [website](https://bidsschematools.readthedocs.io/en/latest/?badge=latest)
+where you will also find the documentation for the python package
+to interact with the schema, [bidsschematools](https://pypi.org/project/bidsschematools/).
## Is your data type not covered in the current BIDS specification?
-BIDS extensions proposals [(BEPs)](../extensions/beps.md) aim to extend the BIDS specification to new data types. A list of extensions ongoing and completed proposals can be found [here](../extensions/beps.md).
+BIDS extensions proposals [(BEPs)](../extensions/beps.md)
+aim to extend the BIDS specification to new data types.
+A list of extensions ongoing and completed proposals can be found [here](../extensions/beps.md).
-Guidelines for contributing to these extensions or starting your own can be found in the [BIDS Extension Proposals Guide](../extensions/index.md).
+Guidelines for contributing to these extensions or starting your own can be found
+in the [BIDS Extension Proposals Guide](../extensions/index.md).
-If only part of your data is covered under BIDS, an option to allow additional files currently not covered in BIDS to pass the validator is the [.bidsignore](https://github.com/bids-standard/legacy-validator/blob/master/bids-validator/README.md) file, which works just like [.gitignore](https://git-scm.com/docs/gitignore). It allows you to list all the files (or directories, with wildcards) that are not BIDS compliant and should be ignored by the validator. Of course you should still try to adhere to upcoming BEPs and the general BIDS philosophy for file names and metadata where possible, but this gives a little extra flexibility.
+If only part of your data is covered under BIDS,
+an option to allow additional files
+currently not covered in BIDS to pass the validator is
+the [.bidsignore](https://github.com/bids-standard/legacy-validator/blob/master/bids-validator/README.md) file,
+which works just like [.gitignore](https://git-scm.com/docs/gitignore).
+It allows you to list all the files (or directories, with wildcards)
+that are not BIDS compliant and should be ignored by the validator.
+Of course you should still try to adhere to upcoming BEPs
+and the general BIDS philosophy for file names and metadata where possible,
+but this gives a little extra flexibility.
## What does [this word] mean?
-We're building a glossary to de-jargonise some of the terms you need to know to work with data in BIDS format. Check it out [here](../getting_started/resources/glossary.md).
+We're building a glossary to de-jargonise some of the terms you need to know to
+work with data in BIDS format. Check it out [here](../getting_started/resources/glossary.md).
## What is a `json` file?
-You can find more information about `json` (and `tsv`) files in the [Metadata-file-formats](../getting_started/folders_and_files/metadata/json.md) page.
+You can find more information about `json` (and `tsv`) files in the
+[Metadata-file-formats](../getting_started/folders_and_files/metadata/json.md) page.
## What liense should I choose for my dataset?
-If you want to know more about what license to choose for your dataset, see the [turing way](https://the-turing-way.netlify.app/reproducible-research/licensing/licensing-data.html#data-licenses) page dedicated to this topic.
+If you want to know more about what license to choose for your dataset,
+see the [turing way](https://the-turing-way.netlify.app/reproducible-research/licensing/licensing-data.html#data-licenses)
+page dedicated to this topic.
-If you plan to put your dataset on [openneuro][openneuro], you should use a CC0 or a PDDL license as explained in their [FAQ](https://openneuro.org/faq).
+If you plan to put your dataset on [openneuro](https://openneuro.org/),
+you should use a CC0 or a PDDL license as explained in their [FAQ](https://openneuro.org/faq).
diff --git a/docs/getting_started/resources/glossary.md b/docs/getting_started/resources/glossary.md
index e25e2a99..f0d79853 100644
--- a/docs/getting_started/resources/glossary.md
+++ b/docs/getting_started/resources/glossary.md
@@ -3,7 +3,7 @@
## Simple definitions for any BIDS related terms
Make sure to also check the
-[official glossary](https://bids-specification.readthedocs.io/en/latest/glossary.html)
+[official glossary](https://bids-specification.readthedocs.io/en/latest/99-appendices/14-glossary.html)
that lists all the terms of the BIDS specification.
We know that when you're getting started with something new there are often jargon-y words
diff --git a/docs/getting_started/tutorials/annotation.md b/docs/getting_started/tutorials/annotation.md
index f536f858..720a9bc0 100644
--- a/docs/getting_started/tutorials/annotation.md
+++ b/docs/getting_started/tutorials/annotation.md
@@ -2,9 +2,17 @@
## What is an annotation?
-Annotation refers to metadata that is directly associated with data. Without adequate annotation, your valuable shared data may be of limited use to other researchers and to you in the future.
-
-While the BIDS requirements for annotation are limited, BIDS supports a framework for inserting comprehensive data annotation at several levels in the dataset. For example, BIDS supports annotations of events and subject characteristics using [Hierarchical Event Descriptors (HED)](https://hed-examples.readthedocs.io/en/latest/index.html), an infrastructure and controlled vocabulary for producing standardized machine-actionable annotations.
+Annotation refers to metadata that is directly associated with data.
+Without adequate annotation, your valuable shared data may be of limited
+use to other researchers and to you in the future.
+
+While the BIDS requirements for annotation are limited,
+BIDS supports a framework for inserting comprehensive
+data annotation at several levels in the dataset.
+For example, BIDS supports annotations of events and subject characteristics using
+[Hierarchical Event Descriptors (HED)](https://hed-examples.readthedocs.io/en/latest/index.html),
+an infrastructure and controlled vocabulary for
+producing standardized machine-actionable annotations.
This tutorial provides a step-by-step process for data annotation in the BIDS framework.
@@ -14,104 +22,170 @@ Annotations in BIDS can be done at several levels, including the dataset, subjec
### Dataset sourcing (`dataset_description.json`)
-`dataset_description.json` is a top-level file that gives details about the source of the dataset, funding, and citation information. This file does not provide any actual description of the data.
+`dataset_description.json` is a top-level file that gives details about the source of the dataset,
+funding, and citation information.
+This file does not provide any actual description of the data.
> You can fill in this blank [dataset description template](../templates/index.md#dataset_descriptionjson) or use it as a guide.
### Dataset description (`README`)
-
-`README` file is a top-level text file that gives the actual overview of the dataset. A comprehensive `README` is essential for users of your data.
+`README` file is a top-level text file that gives the actual overview of the dataset.
+A comprehensive `README` is essential for users of your data.
> You can edit the [README template](../templates/index.md#readmemd) with the vital information needed for others to analyze your dataset.
## Subject annotations
+Annotations at the subject level can be done in the `participants.tsv` file,
+which is a top-level tab-separated value file that provides
+subject information such as age, sex, and handedness.
+Each subject in the dataset should have a row in `participants.tsv`.
-Annotations at the subject level can be done in the `participants.tsv` file, which is a top-level tab-separated value file that provides subject information such as age, sex, and handedness. Each subject in the dataset should have a row in `participants.tsv`.
-
-Each type of metadata is provided in a column in this file, and the nature of the column data is described in the top-level `participants.json` file.
+Each type of metadata is provided in a column in this file,
+and the nature of the column data is described in the top-level
+`participants.json` file.
-Other subject information such as diagnosis or group may be provided in the `participants.tsv` and its corresponding `participants.json` files. Any such information makes your data more valuable to users.
+Other subject information such as diagnosis or group may be provided
+in the `participants.tsv` and its corresponding `participants.json` files.
+Any such information makes your data more valuable to users.
-> You can edit the [participants.tsv template](https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/participants.tsv) and the corresponding [participants.json template](https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/participants.json) to provide this information.
+> You can edit the [participants.tsv template](https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/participants.tsv) and the corresponding
+[participants.json template](https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/participants.json)
+to provide this information.
-If the dataset includes multiple sets of participant level measurements see the BIDS guidelines for adding [phenotypic and assessment data](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#phenotypic-and-assessment-data).
+If the dataset includes multiple sets of participant level measurements see the BIDS guidelines
+for adding [phenotypic and assessment data](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#phenotypic-and-assessment-data).
## Session annotations
-At the session level, the optional `sessions.tsv` and `sessions.json` files can be used to add annotations that apply to an entire session.
+At the session level, the optional `sessions.tsv` and `sessions.json` files can be used to add
+annotations that apply to an entire session.
## Scans/run annotations
-At the scans or run level, the optional `scans.tsv` and `scans.json` files can be used to add annotations that apply to an entire run.
+At the scans or run level, the optional `scans.tsv` and `scans.json` files can be used to add
+annotations that apply to an entire run.
## Event annotations
### Why is event annotation necessary?
+Events provide the crucial linkage between what happens in the experiment
+and the data itself.
+Without the information provided by the dataset events,
+many types of datasets cannot be analyzed.
-Events provide the crucial linkage between what happens in the experiment and the data itself. Without the information provided by the dataset events, many types of datasets cannot be analyzed.
-
-Beyond marking experimental stimuli, participant responses, instructions, and feedback, events can also mark the initiation and termination of tasks and experimental conditions.
+Beyond marking experimental stimuli, participant responses, instructions,
+and feedback, events can also mark the initiation and termination of tasks and experimental conditions.
### BIDS event infrastructure
-Events in BIDS are marked by providing `events.tsv` files associated with data recordings. These tab-separated files have rows corresponding to the individual event markers and columns corresponding to information about the corresponding event.
+Events in BIDS are marked by providing `events.tsv` files associated with data recordings.
+These tab-separated files have rows corresponding to the individual event markers and
+columns corresponding to information about the corresponding event.
#### BIDS minimum requirements
-
-BIDS requires that `events.tsv` files have an `onset` column marking the time of the time that the event occurred in seconds relative to the start of the correspondingly named data recording file. The `events.tsv` files must also have a `duration` column indicating the duration of the event in seconds. At the present time, many datasets model events as instantaneous and use `n/a` in the duration column.
-
-Usually, `events.tsv` files have additional columns containing information about the events. Optional columns include `sample`, `trial_type`, `response_time`, `value`, and `HED`.
-
-The `events.tsv` files **may** contain an arbitrary number of additional columns. All the optional columns are dataset-specific and will be meaningless to dataset users without additional documentation.
-
-BIDS **allows**, but **does not require** documentation about the meanings of the `events.tsv` file columns in similarly-named `events.json` files referred to as JSON sidecars.
+BIDS requires that `events.tsv` files have an `onset` column marking the
+time of the time that the event occurred in seconds relative to the start
+of the correspondingly named data recording file.
+The `events.tsv` files must also have a `duration` column indicating
+the duration of the event in seconds.
+At the present time, many datasets model events as instantaneous
+and use `n/a` in the duration column.
+
+Usually, `events.tsv` files have additional columns containing
+information about the events. Optional columns include `sample`,
+`trial_type`, `response_time`, `value`, and `HED`.
+
+The `events.tsv` files **may** contain an arbitrary number of additional columns.
+All the optional columns are dataset-specific
+and will be meaningless to dataset users
+without additional documentation.
+
+BIDS **allows**, but **does not require** documentation about the meanings
+of the `events.tsv` file columns in similarly-named
+`events.json` files referred to as JSON sidecars.
#### Text descriptions of events
+The BIDS JSON sidecar format accommodates text descriptions of the meanings
+and contents of event file columns in the
+`Description` and `Levels` keys.
-The BIDS JSON sidecar format accommodates text descriptions of the meanings and contents of event file columns in the `Description` and `Levels` keys.
-
-At a minimum, good text descriptions of the event file columns are needed in order for users to use the data correctly.
+At a minimum, good text descriptions of the event file columns are needed in order
+for users to use the data correctly.
#### Machine actionable annotation with HED
-The difficulty with just providing text descriptions of the event file columns and their contents is that users will usually be required to write custom code to use your data.
+The difficulty with just providing text descriptions of the
+event file columns and their contents is that users will usually
+be required to write custom code to use your data.
-BIDS supports [Hierarchical Event Descriptors (HED)](https://www.hed-resources.org), which is an infrastructure and a controlled vocabulary that allows you to annotate your events in a manner that can be used directly by tools.
+BIDS supports [Hierarchical Event Descriptors (HED)](https://www.hed-resources.org),
+which is an infrastructure and a controlled vocabulary that allows you to
+annotate your events in a manner that can be used directly by tools.
-**Remember:** Most users will not be able to work with your dataset without having meaningful information about the dataset events.
+**Remember:** Most users will not be able to work with your dataset
+without having meaningful information about the dataset events.
#### Additional information
+See [Task events](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/05-task-events.html) and
+[Appendix III: Hierarchical Event Descriptors](https://bids-specification.readthedocs.io/en/stable/99-appendices/03-hed.html)
+in the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/)
+for an overview of events before getting started with your own annotation.
-See [Task events](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/05-task-events.html) and [Appendix III: Hierarchical Event Descriptors](https://bids-specification.readthedocs.io/en/stable/appendices/hed.html) in the [BIDS specification][specification] for an overview of events before getting started with your own annotation.
-
-The next section provides an overview of the event annotation process and links to helpful guides and tutorials with the details.
+The next section provides an overview of the event annotation process
+and links to helpful guides and tutorials with the details.
### The event annotation process
-The goal of event annotation is to provide information about events needed for effective and correct data analysis.
+The goal of event annotation is to provide information about
+events needed for effective and correct data analysis.
-Ideally, most of this information should be in a single `events.json` sidecar file located in the root directory of your dataset, where it is easy to find and update.
+Ideally, most of this information should be in a single `events.json` sidecar file
+located in the root directory of your dataset,
+where it is easy to find and update.
-An overview of how event annotation works in BIDS as well as tutorials about using available online tools to facilitate annotation can be found in the [BIDS annotation quickstart](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html).
+An overview of how event annotation works in BIDS as well as tutorials
+about using available online tools to facilitate annotation can be found in the
+[BIDS annotation quickstart](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html).
-There are several online tools available at [HED Tools Online](https://hedtools.org) to help you during this process:
+There are several online tools available at
+[HED Tools Online](https://hedtools.org)
+to help you during this process:
-1. You can extract a ready-to-fill-in JSON sidecar template from a representative `events.tsv` file in your BIDS dataset. A step-by-step tutorial for doing this can be found in the [Create a JSON template tutorial](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html#create-a-json-template).
+1. You can extract a ready-to-fill-in JSON sidecar template
+ from a representative `events.tsv` file in your BIDS dataset.
+ A step-by-step tutorial for doing this can be found in the
+ [Create a JSON template tutorial](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html#create-a-json-template).
-1. Once you have a template, you can start editing the template directory, or you can convert the template to a spreadsheet and edit your annotations in Excel or another tool. Instructions for doing this are available in the [Spreadsheet templates tutorial](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html#spreadsheet-templates).
+1. Once you have a template, you can start editing the template directory,
+ or you can convert the template to a spreadsheet and edit your
+ annotations in Excel or another tool.
+ Instructions for doing this are available in the
+ [Spreadsheet templates tutorial](https://www.hed-resources.org/en/latest/BidsAnnotationQuickstart.html#spreadsheet-templates).
-This process and templates make it convenient to provide basic descriptions, as well as HED tags for your dataset events.
+This process and templates make it convenient to provide basic
+descriptions, as well as HED tags for your dataset events.
-A [HED annotation quickstart](https://www.hed-resources.org/en/latest/HedAnnotationQuickstart.html) outlines a step-by-step process for selecting HED tags during the annotation process.
+A [HED annotation quickstart](https://www.hed-resources.org/en/latest/HedAnnotationQuickstart.html)
+outlines a step-by-step process for selecting HED tags during the annotation process.
#### HED schemas
-The HED tags used to annotate data come from a controlled vocabulary called a HED schema. A HED schema is a structured vocabulary of terms consisting of top-level tags representing general categories in this vocabulary. Each top-level tag is the root of a tree containing tags falling into that category. This structure allows detailed and accurate annotation of events, machine validation of the annotations, and event description-based search across data collected in various studies.
+The HED tags used to annotate data come from a controlled vocabulary called a HED schema.
+A HED schema is a structured vocabulary of terms consisting of top-level tags representing general categories in this vocabulary.
+Each top-level tag is the root of a tree containing tags falling into that category.
+This structure allows detailed and accurate annotation of events,
+machine validation of the annotations,
+and event description-based search across data collected in various studies.
The rules for HED schema vocabularies and HED-compliant tools can be found in the [HED Specification](https://hed-specification.readthedocs.io/en/latest/).
#### HED library schemas
-The HED standard schema contains basic terms that are common across most human neuroimaging, behavioral, and physiological experiments. The HED ecosystem schema libraries extend the standard HED schema with structured vocabularies, including terms unique to specific research fields. This allows the expansion of the HED vocabulary in a scalable manner to support specialized data annotations, for instance, electrophysiological events ([HED-SCORE](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/score)) or language stimuli ([LISA](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/lang)).
+The HED standard schema contains basic terms that are common across most human neuroimaging, behavioral, and physiological experiments.
+The HED ecosystem schema libraries extend the standard HED schema with structured vocabularies, including terms unique to specific research fields.
+This allows the expansion of the HED vocabulary in a scalable manner to support specialized data annotations,
+for instance, electrophysiological events ([HED-SCORE](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/score)) or language stimuli ([LISA](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/lang)).
-Additional details about particular schemas can be found on the [HED schemas](https://hed-schemas.readthedocs.io/en/latest/index.html) documentation page. See [HED schema developer’s guide](https://www.hed-resources.org/en/latest/HedSchemaDevelopersGuide.html) to begin developing your own library schema or contribute to existing HED vocabularies.
+Additional details about particular schemas can be found on the [HED schemas](https://hed-schemas.readthedocs.io/en/latest/index.html) documentation page.
+See [HED schema developer’s guide](https://www.hed-resources.org/en/latest/HedSchemaDevelopersGuide.html)
+to begin developing your own library schema or contribute to existing HED vocabularies.
diff --git a/docs/impact/index.md b/docs/impact/index.md
index e73497d7..32761794 100644
--- a/docs/impact/index.md
+++ b/docs/impact/index.md
@@ -1,100 +1,162 @@
# BIDS Impact
-The Brain Imaging Data Structure (BIDS) is an open global community driving the standardization of neuroscience data across a broad and growing range of modalities and health research disciplines. First released in June 2016, it is supported by a worldwide research network and endorsed by organizations like the International Neuroinformatics Coordinating Facility ([INCF](https://www.incf.org/)).
+The Brain Imaging Data Structure (BIDS) is an open global community driving the
+standardization of neuroscience data across a broad and growing range of modalities
+and health research disciplines. First released in June 2016, it is supported by a
+worldwide research network and endorsed by organizations like the International
+Neuroinformatics Coordinating Facility ([INCF](https://www.incf.org/)).
BIDS encompasses:
-- Over 40 domain-specific and modality-specific technical specifications across scientific and technical domains.
+- Over 40 domain-specific and modality-specific technical specifications
+ across scientific and technical domains.
-- 100+ sample data models for BIDS specifications in the [bids-examples](../datasets/examples.md). Read more about the [BIDS specification][specification].
+- 100+ sample data models for BIDS specifications
+ in the [bids-examples](../datasets/examples.md).
+ Read more about the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/).
-- 2000 open datasets across repositories including [OpenNeuro](https://www.openneuro.org). Read more about [BIDS Datasets](../datasets/index.md).
+- 2000 open datasets across repositories
+ including [OpenNeuro](https://www.openneuro.org).
+ Read more about [BIDS Datasets](../datasets/index.md).
-- Open software conversion and analytics tools, and global infrastructure for collaborating on emerging standards in neuroscience [Poldrack, et al, 2024](https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00103/119672/The-past-present-and-future-of-the-brain-imaging).
+- Open software conversion and analytics tools,
+ and global infrastructure for collaborating on emerging standards in neuroscience
+ [Poldrack, et al, 2024](https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00103/119672/The-past-present-and-future-of-the-brain-imaging).
-- ~ 30,000 annual website visits from a very large community of neuroscience researchers actively consulting the BIDS specifications (April 2023-24).
+- ~ 30,000 annual website visits from a very large community of neuroscience researchers
+ actively consulting the BIDS specifications (April 2023-24).
-- Over 300 BIDS contributors currently supporting and maintaining BIDS community resources and tools.
+- Over 300 BIDS contributors currently supporting
+ and maintaining BIDS community resources and tools.
-- Open working processes through online collaborative tools including GitHub, GitHub Pages, ReadTheDocs, Google Docs, and OSF.
+- Open working processes through online collaborative tools
+ including GitHub, GitHub Pages, ReadTheDocs, Google Docs, and OSF.
-The BIDS core steering and maintainers groups work with the community to optimize open adherence to FAIR principles (Findable, Accessible, Interoperable, and Reusable, [Wilkinson, et al, 2016](https://www.nature.com/articles/sdata201618)) and to actively lower barriers to adoption.
+The BIDS core steering and maintainers groups work with the community to optimize open
+adherence to FAIR principles (Findable, Accessible, Interoperable, and Reusable,
+[Wilkinson, et al, 2016](https://www.nature.com/articles/sdata201618)) and to actively
+lower barriers to adoption.
## BIDS History
-Since its origin, the BIDS standard has revolutionized the way in which neuroimaging research is done. The origin of the BIDS standard is commonly traced back to 2014, when a social media post ignited a deeper discussion about a new way of sharing data, that would ultimately lead to a set of standards that would improve scientific collaboration efforts.
+Since its origin, the BIDS standard has revolutionized the way in which neuroimaging
+research is done. The origin of the BIDS standard is commonly traced back to 2014,
+when a social media post ignited a deeper discussion about a new way of sharing
+data, that would ultimately lead to a set of standards that would improve scientific
+collaboration efforts.
-Following this initial discussion (and on the shoulders of many many volunteer hours by maintainers and the community at large) the BIDS standard saw significant adoption in the neuroimaging research landscape and continues to expand every day. A more complete history and discussion about the future of the BIDS landscape can be found in this [recent publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC10516110/).
+Following this initial discussion (and on the shoulders of many many volunteer hours
+by maintainers and the community at large) the BIDS standard saw significant adoption
+in the neuroimaging research landscape and continues to expand every day. A more complete
+history and discussion about the future of the BIDS landscape can be found in this
+[recent publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC10516110/).
-The BIDS standard continues to be adopted by a larger share of the community each year. We have seen a large and growing number of visitors to the BIDS website. A large number of BIDS users also continue to explore the BIDS Specification and contribute to the community every month.
+The BIDS standard continues to be adopted by a larger share of the community each year.
+We have seen a large and growing number of visitors to the BIDS website. A large number of
+BIDS users also continue to explore the BIDS Specification and contribute to the community every month.
-We also document centers, institutes, and databases around the world that have implemented BIDS as their organizational structure. While the list continues to grow, an initial list of centers and the associated BIDS initiatives or database can be found [here](https://docs.google.com/spreadsheets/d/1aySjPpEGGQwFcOavkQdcvk2t2UMXt_zoTzWLWUmq20M/edit#gid=0).
+We also document centers, institutes, and databases around the world that have implemented BIDS as
+their organizational structure. While the list continues to grow, an initial list of centers and the associated
+BIDS initiatives or database can be found
+[here](https://docs.google.com/spreadsheets/d/1aySjPpEGGQwFcOavkQdcvk2t2UMXt_zoTzWLWUmq20M/edit#gid=0).
### Website and Specification traffic dashboards
-In order to measure the volume of traffic to our website and the [ReadTheDocs rendering of the specification][specification], we utilize Google Analytics.
+In order to measure the volume of traffic to our website and the
+[ReadTheDocs rendering of the specification](https://bids-specification.readthedocs.io/en/stable/),
+we utilize Google Analytics.
For visualizing our metrics, we have put together 2 dashboards:
1. [the website](https://datastudio.google.com/u/0/reporting/eab164ba-9f98-46e8-bee8-1f4f5328dc6e/page/V5leB)
1. [the specification](https://datastudio.google.com/u/0/reporting/57bf46f1-034c-4d8b-9fe2-3a2243e469c5/page/w1leB)
-The default time period is set to the past 6 months. This can be changed by adjusting the time period in the upper left corner. Please feel free to use any of these figures in your grant! If there are additional statistics not currently conveyed, please reach out to or the BIDS maintainers via a GitHub issue, or by email ([bids.maintenance@gmail.com](mailto:bids.maintenance@gmail.com)).
+The default time period is set to the past 6 months. This can be changed by
+adjusting the time period in the upper left corner. Please feel free to use any
+of these figures in your grant! If there are additional statistics not currently
+conveyed, please reach out to or the BIDS maintainers via a GitHub issue, or by email
+ ([bids.maintenance@gmail.com](mailto:bids.maintenance@gmail.com)).
### BIDS usage
-We ran [a survey](https://reproducibility.stanford.edu/bids-usage-survey-results/) in June 2019 to evaluate the uptake of BIDS in the community. We received feedback from 116 global researchers.
+We ran
+[a survey](https://reproducibility.stanford.edu/bids-usage-survey-results/) in
+June 2019 to evaluate the uptake of BIDS in the community. We received feedback
+from 116 global researchers.
-We have a [google doc](https://docs.google.com/spreadsheets/d/1aySjPpEGGQwFcOavkQdcvk2t2UMXt_zoTzWLWUmq20M/edit#gid=0) that is crowdsourcing imaging centers, institutes, databases around the world that have implemented BIDS as their organizational structure.
+We have a
+[google doc](https://docs.google.com/spreadsheets/d/1aySjPpEGGQwFcOavkQdcvk2t2UMXt_zoTzWLWUmq20M/edit#gid=0)
+that is crowdsourcing imaging centers, institutes, databases around the world
+that have implemented BIDS as their organizational structure.
-We also measured the general BIDS impact across multiple domains (datasets, citations...). Read more on the [Impact Dashboards page](./measuring.md).
+We also measured the general BIDS impact across multiple domains (datasets, citations...).
+Read more on the [Impact Dashboards page](./measuring.md).
### Neurostars
-We also track the interest and usage of the BIDS standard via discussions on Neurostars to help us estimate trends in usage. Below is a snapshot as of ??? (date).
-
+We also track the interest and usage of the BIDS standard via discussions on Neurostars
+to help us estimate trends in usage. Below is a snapshot as of ??? (date).
-| tag | nb topics | nb posts | topics with no reply | topics with answer |
-| :-- | --: | --: | --: | --: |
-| bids | 716 | 3404 | 114 | 211 |
-| bids-validator | 80 | 488 | 1 | 28 |
-| pybids | 29 | 175 | 3 | 12 |
-| dcm2bids | 92 | 529 | 4 | 53 |
-| heudiconv | 102 | 454 | 17 | 23 |
-| mriqc | 141 | 604 | 32 | 37 |
-| fmriprep | 1286 | 7727 | 145 | 445 |
-| qsiprep | 170 | 1063 | 12 | 76 |
-| aslprep | 21 | 74 | 5 | 8 |
-| nilearn | 585 | 2454 | 90 | 182 |
-| fitlins | 19 | 129 | 2 | 5 |
-| openneuro | 95 | 479 | 15 | 28 |
+| tag | nb topics | nb posts | topics with no reply | topics with answer |
+|:---------------|----------:|---------:|---------------------:|-------------------:|
+| bids | 716 | 3404 | 114 | 211 |
+| bids-validator | 80 | 488 | 1 | 28 |
+| pybids | 29 | 175 | 3 | 12 |
+| dcm2bids | 92 | 529 | 4 | 53 |
+| heudiconv | 102 | 454 | 17 | 23 |
+| mriqc | 141 | 604 | 32 | 37 |
+| fmriprep | 1286 | 7727 | 145 | 445 |
+| qsiprep | 170 | 1063 | 12 | 76 |
+| aslprep | 21 | 74 | 5 | 8 |
+| nilearn | 585 | 2454 | 90 | 182 |
+| fitlins | 19 | 129 | 2 | 5 |
+| openneuro | 95 | 479 | 15 | 28 |
### Mailing list volume
-As of July 1, 2020, we have 183 people signed up for our [BIDS email list](https://forms.gle/JFo2aEkYbKY4EbmE6) and 412 members on our [google group][bids_google_group].
+As of July 1, 2020, we have 183 people signed up for our
+[BIDS email list](https://forms.gle/JFo2aEkYbKY4EbmE6) and 412 members on our
+[google group](https://groups.google.com/forum/#!forum/bids-discussion).
## How the BIDS team can help you
-If you are in the process of putting together a grant, **please email/message the pillar lead** that is most closely associated with your proposed grant or the BIDS maintainers email ([bids.maintenance@gmail.com](mailto:bids.maintenance@gmail.com)) so we may help support this. Our organization is structured into 3 pillars: standard, tools, and collaboration.
+If you are in the process of putting together a grant, **please email/message
+the pillar lead** that is most closely associated with your proposed grant or the
+BIDS maintainers email ([bids.maintenance@gmail.com](mailto:bids.maintenance@gmail.com))
+so we may help support this. Our organization is structured into 3 pillars: standard,
+tools, and collaboration.
-Our range of support covers activities such as: meeting with the Steering and Maintainers Groups to assisting with connecting you with other BIDS grant writers or related initiatives to receiving a letter of support from the Steering Group.
+Our range of support covers activities such as: meeting with the Steering and
+Maintainers Groups to assisting with connecting you with other BIDS grant
+writers or related initiatives to receiving a letter of support from the
+Steering Group.
-Regarding **requesting a letter of support** - please submit a drafted letter of support to the collaboration lead or the BIDS maintainers email ([bids.maintenance@gmail.com](mailto:bids.maintenance@gmail.com)) so we may review internally.
+Regarding **requesting a letter of support** - please submit a drafted letter of
+support to the collaboration lead or the BIDS maintainers email
+([bids.maintenance@gmail.com](mailto:bids.maintenance@gmail.com)) so we may review internally.
-Please include how you plan on giving back to the BIDS community. The primary mechanism is to support a member of your team to become a BIDS Maintainer. Letters of support are approved by the Steering Group. This process may take 2-4 weeks to complete.
+Please include how you plan on giving back to the BIDS community. The primary
+mechanism is to support a member of your team to become a BIDS Maintainer.
+Letters of support are approved by the Steering Group. This process may take 2-4
+weeks to complete.
-We kindly ask you to please **share your grant online** - successful or not. This will signal to the rest of the community what avenues we have pursued and what our fellow colleagues are planning on doing next. These can be grants that directly extend our support into a new domain, grants that help BIDS (for example OpenNeuro), or unsuccessful grant applications.
+We kindly ask you to please **share your grant online** - successful or not.
+This will signal to the rest of the community what avenues we have pursued and
+what our fellow colleagues are planning on doing next. These can be grants that
+directly extend our support into a new domain, grants that help BIDS (for example
+OpenNeuro), or unsuccessful grant applications.
For example, please find our [NIH-R24 Brain Initiative BIDS-Derivatives grant](https://osf.io/c3dgx/).
A listing of the previous grants can be found [here](../collaboration/acknowledgments.md)
## Citing BIDS in your project
-
-You can find information on citing BIDS standards for specific modalities and citing BIDS in general [in the specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids)
+You can find information on citing BIDS standards for specific modalities and
+citing BIDS in general
+[in the specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids)
-
the [starter kit](./getting_started/index.md) with a simple explanation how to work with it,
-
-
-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](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](https://openneuro.org/) 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.
+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
@@ -46,50 +64,67 @@ Another part is that BIDS is striving to not reinventing other standards and met
-- :material-account-group:{ .lg .middle } **For the public good**
+- :material-account-group:{ .lg .middle } **For the public good**
- ***
+ ---
- - Lowers scientific waste
- - Gives opportunity to less-funded researchers
- - Improves efficiency
- - Spurs innovation
+ - Lowers scientific waste
+ - Gives opportunity to less-funded researchers
+ - Improves efficiency
+ - Spurs innovation
-- :recycle:{ .lg .middle } **For yourself**
+- :recycle:{ .lg .middle } **For yourself**
- ***
+ ---
- - You are likely the future user of the data and data analysis pipelines you’ve developed
+ - You are likely the future user of the data and data analysis pipelines you’ve developed
- - Enables and simplifies collaboration
+ - Enables and simplifies collaboration
- - Reviewers and funding agencies like to see reproducible results
+ - 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.)
+ - Open-science based funding opportunities and awards available
+ (for instance: OHBM Replication Award, Mozilla Open Science Fellowship,
+ Google Summer of Code, and so on.)
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.
+- 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.
+- 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.
+- 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.
+- 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 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).
+- 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).
-- Look through some of the community's [presentations on BIDS](https://osf.io/yn93h/).
+- 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).
+- 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 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).
+- 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:**
diff --git a/docs/standards/bids_specification/index.md b/docs/standards/bids_specification/index.md
index 993c43cf..828f1fed 100644
--- a/docs/standards/bids_specification/index.md
+++ b/docs/standards/bids_specification/index.md
@@ -1,7 +1,10 @@
# The BIDS specification
-The Brain Imaging Data Structure specification can be [browsed online][specification].
+The Brain Imaging Data Structure specification can be [browsed online](https://bids-specification.readthedocs.io/en/stable/).
-PDF versions of the specification can be found on zenodo at [https://doi.org/10.5281/zenodo.10175845](https://doi.org/10.5281/zenodo.10175845) for BIDS versions >= 1.9.
+PDF versions of the specification
+can be found on zenodo at [https://doi.org/10.5281/zenodo.10175845](https://doi.org/10.5281/zenodo.10175845)
+for BIDS versions >= 1.9.
-Previous releases of the PDF version of the BIDS specification (versions 1.0.0 to 1.8.0) can be found in [this Zenodo record](https://zenodo.org/doi/10.5281/zenodo.3686061).
+Previous releases of the PDF version of the BIDS specification (versions 1.0.0 to 1.8.0)
+can be found in [this Zenodo record](https://zenodo.org/doi/10.5281/zenodo.3686061).
diff --git a/docs/tools/validator.md b/docs/tools/validator.md
index e30115e6..fe35b688 100644
--- a/docs/tools/validator.md
+++ b/docs/tools/validator.md
@@ -1,13 +1,18 @@
# BIDS validation
-The [BIDS Validator](https://github.com/bids-standard/bids-validator) is a tool that checks if a dataset is compliant with the BIDS standard. The validator is available for use within several different environments to best suit individual user preferences and use cases, those versions are:
+The [BIDS Validator](https://github.com/bids-standard/bids-validator) is a tool
+that checks if a dataset is compliant with the BIDS standard.
+The validator is available for use within several different environments
+to best suit individual user preferences and use cases, those versions are:
-- [A web browser based version](https://bids-standard.github.io/bids-validator/)
-- [Command line version](https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html)
-- [Docker based version](https://hub.docker.com/r/bids/validator)
-- A [python library](https://github.com/bids-standard/python-validator) installable from [pypi](https://pypi.org/project/bids-validator/) or [conda-forge](https://anaconda.org/conda-forge/bids-validator)
+- [A web browser based version](https://bids-standard.github.io/bids-validator/)
+- [Command line version](https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html)
+- [Docker based version](https://hub.docker.com/r/bids/validator)
+- A [python library](https://github.com/bids-standard/python-validator) installable from [pypi](https://pypi.org/project/bids-validator/) or [conda-forge](https://anaconda.org/conda-forge/bids-validator)
-Instructions to install and use these versions can be found within the [quickstart guide](https://github.com/bids-standard/bids-validator) at the BIDS Validator repository.
+Instructions to install and use these versions can be found
+within the [quickstart guide](https://github.com/bids-standard/bids-validator)
+at the BIDS Validator repository.
!!! note
@@ -16,11 +21,14 @@ Instructions to install and use these versions can be found within the [quicksta
## Data Privacy and Confidentiality
-Please note that the web app is entirely browser (not server) based. As such, there is no file uploading as part of the validation.
+Please note that the web app is entirely browser (not server) based.
+As such, there is no file uploading as part of the validation.
## Browser Version
-1. The BIDS Validator can be found at . It requires that you use the Chrome or Firefox browser, since those are the only ones in which you can select a whole folder rather than individual files.
+1. The BIDS Validator can be found at .
+ It requires that you use the Chrome or Firefox browser,
+ since those are the only ones in which you can select a whole folder rather than individual files.
@@ -53,7 +61,9 @@ Please note that the web app is entirely browser (not server) based. As such, th
### Verifying a BIDS compliant data set
-After [installation with deno](https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html#using-the-command-line) using the CLI is relatively simple. Locate a bids data set similar to the one below:
+After [installation with deno](https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html#using-the-command-line)
+using the CLI is relatively simple.
+Locate a bids data set similar to the one below:
```bash
user@host:~/bids-examples$ tree pet001
@@ -102,7 +112,7 @@ user@host:~/bids-examples$ bids-validator pet001
As stated with the browser version above, one may elect to ignore warnings,
but the information provided via the validator should help to pinpoint
where and how to resolve some of these warnings.
- When in doubt consult the [BIDS specification][specification]
+ When in doubt consult the [BIDS specification](https://bids-specification.readthedocs.io/en/latest/)
```bash
[WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.
#### Tell us a little about your current research focus and experience
-I am currently a researcher at the Neurobiology Research Unit at Rigshospitalet, Copenhagen and have an appointment as an assistant professor at the Department for Computer Science at the University of Copenhagen. My research interests include the application of image processing, computer vision and machine learning techniques in medical imaging as well as the statistical interpretations of results retrieved in medical imaging problems.
+I am currently a researcher at the Neurobiology Research Unit at Rigshospitalet, Copenhagen and have an appointment as an assistant professor at the Department for Computer Science at the University of Copenhagen.
+My research interests include the application of image processing, computer vision and machine learning techniques in medical imaging as well as the statistical interpretations of results retrieved in medical imaging problems.
#### How did you get involved in BIDS?
-In 2016, the NeuroReceptor Mapping conference (NRM2016) in Boston hosted a panel discussion regarding positron emission tomography (PET) data sharing. The audience unanimously supported a motion to establish a working group that would propose guidelines for data sharing. Following this, in fall 2017 I attended NeuroHackWeek in Seattle and met Chris Gorgolewski. Chris had been called in by the PET community to help with data standardization and with adopting a PET BIDS extension. When he heard that I am interested in data sharing and working with PET and was actually located in one of the biggest PET labs worldwide, he asked me if I could help with the development of the [PET BIDS extension (BEP0009)](https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0/edit).
+In 2016, the NeuroReceptor Mapping conference (NRM2016) in Boston hosted a panel discussion regarding positron emission tomography (PET) data sharing.
+The audience unanimously supported a motion to establish a working group that would propose guidelines for data sharing. Following this, in fall 2017 I attended NeuroHackWeek in Seattle and met Chris Gorgolewski.
+Chris had been called in by the PET community to help with data standardization and with adopting a PET BIDS extension.
+When he heard that I am interested in data sharing and working with PET and was actually located in one of the biggest PET labs worldwide, he asked me if I could help with the development of the [PET BIDS extension (BEP0009)](https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0/edit).
#### Why did you choose to run for election to the steering group?
-My biggest motivation for working on BIDS is the aim of facilitating data sharing. Compared to MRI and most other neuroimaging modalities, PET is a very expensive, technically challenging and invasive technique. This leads to sample sizes in general being low (~20-50 people) and to data analysis workflows being highly dependent on the neuroimaging lab that acquires the data. So I am really hoping to get momentum in the PET data sharing world and hence it was a natural interest of mine to get involved in the steering group to represent PET.
+My biggest motivation for working on BIDS is the aim of facilitating data sharing. Compared to MRI and most other neuroimaging modalities, PET is a very expensive, technically challenging and invasive technique. This leads to sample sizes in general being low (~20-50 people) and to data analysis workflows being highly dependent on the neuroimaging lab that acquires the data.
+So I am really hoping to get momentum in the PET data sharing world and hence it was a natural interest of mine to get involved in the steering group to represent PET.
#### What does success look like for BIDS, in your opinion?
-For me that clearly means adoption of BIDS by researchers and sharing of data. Adoption can be in terms of standardizing analysis workflows to be BIDS compatible, but also to storing data locally and on data sharing sites in BIDS format.
+For me that clearly means adoption of BIDS by researchers and sharing of data.
+Adoption can be in terms of standardizing analysis workflows to be BIDS compatible, but also to storing data locally and on data sharing sites in BIDS format.
#### What are you hoping to achieve in the next year?
-My main focus will be on outreach to the communities that are not yet heavily involved in BIDS. For example, compared to the MRI community the PET community needs to reinvent itself and embrace data sharing as recently has been [pointed out in a major PET journal](https://link.springer.com/article/10.1007%2Fs00259-019-04541-y). To this end I am actively involved in organizing a data sharing/BIDS workshop at NRM2020 and to get more PET researchers interested in contributing to and using BIDS. As a steering group member, I want to identify further imaging modalities/derivatives in the need of standardization and get them started on the road to BIDS and support them with embracing BIDS.
+My main focus will be on outreach to the communities that are not yet heavily involved in BIDS.
+For example, compared to the MRI community the PET community needs to reinvent itself and embrace data sharing as recently has been [pointed out in a major PET journal](https://link.springer.com/article/10.1007%2Fs00259-019-04541-y).
+To this end I am actively involved in organizing a data sharing/BIDS workshop at NRM2020 and to get more PET researchers interested in contributing to and using BIDS.
+As a steering group member, I want to identify further imaging modalities/derivatives in the need of standardization and get them started on the road to BIDS and support them with embracing BIDS.
### Robert Oostenveld 
#### Tell us a little about your current research focus and experience
-I am associate PI and MEG physicist at the Donders Institute. My main research interest is in the development of analysis methods for MEG and EEG, although I also work with iEEG, NIRS, (f)MRI and other types of data. About 15 years ago, I initiated the development of the FieldTrip toolbox, triggered by the need in our lab to do state-of-the-art analyses in a reproducible and efficient manner; and to day we continue to develop it with this in mind. I am (co)supervising many cognitive neuroscience students and colleagues; developing open source code and open documentation is for me the way to work efficiently and to share and accumulate knowledge in a wide network.
+I am associate PI and MEG physicist at the Donders Institute.
+My main research interest is in the development of analysis methods for MEG and EEG, although I also work with iEEG, NIRS, (f)MRI and other types of data.
+About 15 years ago, I initiated the development of the FieldTrip toolbox, triggered by the need in our lab to do state-of-the-art analyses in a reproducible and efficient manner; and to day we continue to develop it with this in mind.
+I am (co)supervising many cognitive neuroscience students and colleagues; developing open source code and open documentation is for me the way to work efficiently and to share and accumulate knowledge in a wide network.
#### How did you get involved in BIDS?
-The MEG research community mainly depends on a small number of open source toolboxes: MNE-Python, SPM, BrainStorm and FieldTrip. The developers of these toolboxes share very similar ambitions and goals, and we regularly meet at conferences, workshops or training events. For the MEG extension to BIDS we teamed up to get our knowledge and that of our respective user communities represented. Following the publication of the MEG extension, it was only natural to remain involved in the EEG and iEEG extension.
+The MEG research community mainly depends on a small number of open source toolboxes: MNE-Python, SPM, BrainStorm and FieldTrip.
+The developers of these toolboxes share very similar ambitions and goals, and we regularly meet at conferences, workshops or training events.
+For the MEG extension to BIDS we teamed up to get our knowledge and that of our respective user communities represented.
+Following the publication of the MEG extension, it was only natural to remain involved in the EEG and iEEG extension.
#### Why did you choose to run for election to the steering group?
-Besides developing MEG/EEG methods and tools, I am involved in the research infrastructure and in the data management of our institute at large, which covers many different experimental research questions with different scanners and and experimental set-ups. It is obvious that brain data from imaging methods and electrophysiology needs to be properly managed, but I also find it important that details of cognitive experiments - which often involve multiple behavioral modalities - can be properly documented and shared. Structural and resting state data are important and interesting, but documenting and sharing data acquired in relation to cognition and behavior raises the complexity even further.
+Besides developing MEG/EEG methods and tools, I am involved in the research infrastructure and in the data management of our institute at large, which covers many different experimental research questions with different scanners and and experimental set-ups.
+It is obvious that brain data from imaging methods and electrophysiology needs to be properly managed, but I also find it important that details of cognitive experiments - which often involve multiple behavioral modalities - can be properly documented and shared.
+Structural and resting state data are important and interesting, but documenting and sharing data acquired in relation to cognition and behavior raises the complexity even further.
#### What does success look like for BIDS, in your opinion?
-I hope that BIDS achieves success on multiple levels. One is that many more researchers get over the initial hurdles for sharing data, and for more efficient reuse of data that was shared by others. Another is that the common "vocabulary" - that we are required to develop to organize shared data - will help in developing better research tools, pipelines and strategies. Working together on data increases the awareness and understanding of details in different lab and experimental setups.
+I hope that BIDS achieves success on multiple levels.
+One is that many more researchers get over the initial hurdles for sharing data, and for more efficient reuse of data that was shared by others.
+Another is that the common "vocabulary" - that we are required to develop to organize shared data - will help in developing better research tools, pipelines and strategies.
+Working together on data increases the awareness and understanding of details in different lab and experimental setups.
#### What are you hoping to achieve in the next year?
-The number of stakeholders that either rely on BIDS for their data or for their tool development has grown very rapidly in the last years. I hope that we can improve communication to maintain a considerate, robust and consensus-based development model of the specification. Furthermore, I hope that we can extend BIDS with more raw data types, like eye-tracking, NIRS, PET, genetics, and more behavioral measures, and that we can establish a strategy for documenting and sharing processed data.
+The number of stakeholders that either rely on BIDS for their data or for their tool development has grown very rapidly in the last years.
+I hope that we can improve communication to maintain a considerate, robust and consensus-based development model of the specification.
+Furthermore, I hope that we can extend BIDS with more raw data types, like eye-tracking, NIRS, PET, genetics, and more behavioral measures, and that we can establish a strategy for documenting and sharing processed data.
### Russell Poldrack 
#### Tell us a little about your current research focus and experience
-I am a professor of psychology at Stanford. My main basic research interests are focused on the brain systems involved in decision making and executive function, primarily using fMRI. In the last decade I've become increasingly interested in meta-scientific topics focused on reproducibility and transparency, including involvement in a number of data sharing initiatives including [OpenNeuro][openneuro], [NeuroVault](https://neurovault.org/), and [NeuroSynth](https://neurosynth.org/).
+I am a professor of psychology at Stanford.
+My main basic research interests are focused on the brain systems involved in decision making and executive function, primarily using fMRI.
+In the last decade I've become increasingly interested in meta-scientific topics focused on reproducibility and transparency, including involvement in a number of data sharing initiatives including [OpenNeuro](https://openneuro.org/), [NeuroVault](https://neurovault.org/), and [NeuroSynth](https://neurosynth.org/).
#### How did you get involved in BIDS?
-I was involved in BIDS from its inception. BIDS grew out of an earlier organizational scheme that we had developed for the OpenFMRI project, but its shortcomings were evident, and we wanted to develop a standard that would address a much broader range of needs across the neuroimaging community. I worked closely with Chris Gorgolewski in the development of the first draft of the standard, and have remained involved (though not deeply in the technical trenches) as the standard has blossomed. I've been particularly interested and involved in the [BIDS Derivatives](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/) standards.
+I was involved in BIDS from its inception.
+BIDS grew out of an earlier organizational scheme that we had developed for the OpenFMRI project, but its shortcomings were evident, and we wanted to develop a standard that would address a much broader range of needs across the neuroimaging community.
+I worked closely with Chris Gorgolewski in the development of the first draft of the standard, and have remained involved (though not deeply in the technical trenches) as the standard has blossomed.
+I've been particularly interested and involved in the [BIDS Derivatives](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/) standards.
#### Why did you choose to run for election to the steering group?
-I think that my knowledge of the history and background for BIDS as well as my broader view of the field of neuroimaging puts me in a good position to help guide its growth in the future. I also have lots of experience with management of large projects, which I hope to bring to bear as BIDS matures.
+I think that my knowledge of the history and background for BIDS as well as my broader view of the field of neuroimaging puts me in a good position to help guide its growth in the future.
+I also have lots of experience with management of large projects, which I hope to bring to bear as BIDS matures.
#### What does success look like for BIDS, in your opinion?
-Adoption. A standard is only useful if researchers in the field actually use it. So far that has worked well for BIDS, but I would love to see more support from standard software packages, particularly as the BIDS Derivatives standards mature.
+Adoption.
+A standard is only useful if researchers in the field actually use it.
+So far that has worked well for BIDS, but I would love to see more support from standard software packages, particularly as the BIDS Derivatives standards mature.
#### What are you hoping to achieve in the next year?
@@ -104,27 +154,40 @@ I hope that we can continue a smooth transition to shared governance of the proj
#### Tell us a little about your current research focus and experience
-I'm a research fellow at the Alan Turing Institute. I joined with a research proposal saying I would try to replicate findings looking at brain development and the emergence of mental health conditions in the published literature, but I very quickly found that publications themselves don't share enough information to reproduce their own findings, nevermind doing the same thing in another cohort. So now I work to incentivise reproducible research and contributions into open source communities.
+I'm a research fellow at the Alan Turing Institute.
+I joined with a research proposal saying I would try to replicate findings looking at brain development and the emergence of mental health conditions in the published literature, but I very quickly found that publications themselves don't share enough information to reproduce their own findings, nevermind doing the same thing in another cohort.
+So now I work to incentivise reproducible research and contributions into open source communities.
#### How did you get involved in BIDS?
-I really love the goal of BIDS - life would be so much easier if everyone's data and code were interoperable with each other - but I found the specification itself really difficult to follow. So in 2018 I mentored Patrick Park - a Google Summer of Code student - to develop the [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit). Our goal was to demysify some of the jargon ([what even _is_ a json file?](https://github.com/bids-standard/bids-starter-kit/wiki/Metadata-file-formats#json-files)) and make it easier for folks to get started. I'm also one of the lead developers of the [BEP001 extension](https://github.com/bids-standard/bep001) which is working to include quantitative MRI sequences in the specification.
+I really love the goal of BIDS - life would be so much easier if everyone's data and code were interoperable with each other - but I found the specification itself really difficult to follow.
+So in 2018 I mentored Patrick Park - a Google Summer of Code student - to develop the [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit).
+Our goal was to demysify some of the jargon ([what even _is_ a json file?](https://github.com/bids-standard/bids-starter-kit/wiki/Metadata-file-formats#json-files)) and make it easier for folks to get started. I'm also one of the lead developers of the [BEP001 extension](https://github.com/bids-standard/bep001) which is working to include quantitative MRI sequences in the specification.
#### Why did you choose to run for election to the steering group?
-I have lots of opinions (don't we all), especially about how to build and engage open source communities. I'm particularly interested in expanding the number of people who participate in setting the future directions for BIDS. The project's greatest strength is that the specification is community-led and responsive to their needs. I wanted to join the steering group to see BIDS meet its potential to make the lives of neuroimaging researchers easier around the world.
+I have lots of opinions (don't we all), especially about how to build and engage open source communities.
+I'm particularly interested in expanding the number of people who participate in setting the future directions for BIDS.
+The project's greatest strength is that the specification is community-led and responsive to their needs.
+I wanted to join the steering group to see BIDS meet its potential to make the lives of neuroimaging researchers easier around the world.
#### What does success look like for BIDS, in your opinion?
-Success in my eyes would be that everyone collecting data never had to think about how to save their files. From the minute the data came off the scanner, it would be in a well documented directory structure that was the same as everyone else's. In addition, all those researchers would have access to well documented open source tools to help them explore and summarize the scans they had acquired. Ultimately, I want people working on brain imaging data to be focused on thinking about (and implementing) interesting research questions, not how to find stray typos in the data file names.
+Success in my eyes would be that everyone collecting data never had to think about how to save their files.
+From the minute the data came off the scanner, it would be in a well documented directory structure that was the same as everyone else's.
+In addition, all those researchers would have access to well documented open source tools to help them explore and summarize the scans they had acquired.
+Ultimately, I want people working on brain imaging data to be focused on thinking about (and implementing) interesting research questions, not how to find stray typos in the data file names.
#### What are you hoping to achieve in the next year?
-The first thing I'd like the steering committee to do is map the community and conduct a pluses and deltas exercise: what are the things they like and what would they change? I suspect that the move to communications on GitHub has been difficult for a lot of people - there are many more notifications than when we had discussions on the mailing list and I think people find it hard to keep up. So probably a clearer dissemination system to keep people updated on what's going on would be really helpful.
+The first thing I'd like the steering committee to do is map the community and conduct a pluses and deltas exercise: what are the things they like and what would they change?
+I suspect that the move to communications on GitHub has been difficult for a lot of people - there are many more notifications than when we had discussions on the mailing list and I think people find it hard to keep up.
+So probably a clearer dissemination system to keep people updated on what's going on would be really helpful.
### Thank you from the BIDS Steering Group
-Thank you to [everyone who stood for election](https://docs.google.com/document/d/1yb6j3a90serWbtab7ukSMyecs16sGfYTSGftH-4ArvA/) to this inaugural year of the BIDS steering group. It is a great strength of the community that so many people are committed to the development, maintenance and adoption of the Brain Imaging Data Structure.
+Thank you to [everyone who stood for election](https://docs.google.com/document/d/1yb6j3a90serWbtab7ukSMyecs16sGfYTSGftH-4ArvA/) to this inaugural year of the BIDS steering group.
+It is a great strength of the community that so many people are committed to the development, maintenance and adoption of the Brain Imaging Data Structure.
We are proud to shepherd this community into 2020, and beyond.
diff --git a/docs/blog/posts/v1.9.0-release.md b/docs/blog/posts/v1.9.0-release.md
index 001f7c63..28d9ebd4 100644
--- a/docs/blog/posts/v1.9.0-release.md
+++ b/docs/blog/posts/v1.9.0-release.md
@@ -3,7 +3,7 @@ date: 2023-11-23
slug: "BIDS 1.9.0 released!"
author: BIDS Maintainers
categories:
- - release
+- release
---
We are pleased to announce the release of version 1.9.0 of the Brain Imaging Data Structure (BIDS)!
@@ -18,11 +18,11 @@ We would like to thank contributors to this BEP, led by Sein Jeung and Julius We
Check out the [preprint associated with this BEP](https://osf.io/preprints/psyarxiv/w6z79/).
-Example datasets for motion data can be found on our [BIDS example repository][bids_examples_gh]:
+Example datasets for motion data can be found on our [BIDS example repository](https://github.com/bids-standard/bids-examples):
-- [motion_dualtask](https://github.com/bids-standard/bids-examples/tree/master/motion_dualtask)
-- [motion_spotrotation](https://github.com/bids-standard/bids-examples/tree/master/motion_spotrotation)
-- [motion_systemvalidation](https://github.com/bids-standard/bids-examples/tree/master/motion_systemvalidation)
+- [motion_dualtask](https://github.com/bids-standard/bids-examples/tree/master/motion_dualtask)
+- [motion_spotrotation](https://github.com/bids-standard/bids-examples/tree/master/motion_spotrotation)
+- [motion_systemvalidation](https://github.com/bids-standard/bids-examples/tree/master/motion_systemvalidation)
Motion datasets can already be validated with [the BIDS validator](https://github.com/bids-standard/bids-validator) and queried with libraries like [pybids](https://github.com/bids-standard/pybids) or [bids-matlab](https://github.com/bids-standard/bids-matlab).
@@ -32,23 +32,23 @@ Some of the other notable changes also included in this release:
Filename entities updates:
-- Add an OPTIONAL "chunk" entity to MRI datatype [#1586](https://github.com/bids-standard/bids-specification/pull/1586)
-- Remove atlas entity and replace it with seg in prep of BEP038 [#1579](https://github.com/bids-standard/bids-specification/pull/1579)
-- Allow for an OPTIONAL "echo" entity to be used with T1w and other nonparametric anatomical suffixes [#1570](https://github.com/bids-standard/bids-specification/pull/1570)
-- Adding an OPTIONAL “task” entity to structural MRI acquisitions [#1185](https://github.com/bids-standard/bids-specification/pull/1185)
-- Clarify that data files must be uniquely identified by entities/suffix [#1508](https://github.com/bids-standard/bids-specification/pull/1508)
+- Add an OPTIONAL "chunk" entity to MRI datatype [#1586](https://github.com/bids-standard/bids-specification/pull/1586)
+- Remove atlas entity and replace it with seg in prep of BEP038 [#1579](https://github.com/bids-standard/bids-specification/pull/1579)
+- Allow for an OPTIONAL "echo" entity to be used with T1w and other nonparametric anatomical suffixes [#1570](https://github.com/bids-standard/bids-specification/pull/1570)
+- Adding an OPTIONAL “task” entity to structural MRI acquisitions [#1185](https://github.com/bids-standard/bids-specification/pull/1185)
+- Clarify that data files must be uniquely identified by entities/suffix [#1508](https://github.com/bids-standard/bids-specification/pull/1508)
Metadata updates:
-- Allow Levels field of column descriptions to be objects with TermURLs for each level [#1603](https://github.com/bids-standard/bids-specification/pull/1603)
-- Add "visual correction" and "head stabilization" metadata [#1539](https://github.com/bids-standard/bids-specification/pull/1539)
-- Permit CITATION.cff as structured alternative to some dataset_description fields [#1525](https://github.com/bids-standard/bids-specification/pull/1525)
-- Add screen parameters metadata [#1369](https://github.com/bids-standard/bids-specification/pull/1369)
+- Allow Levels field of column descriptions to be objects with TermURLs for each level [#1603](https://github.com/bids-standard/bids-specification/pull/1603)
+- Add "visual correction" and "head stabilization" metadata [#1539](https://github.com/bids-standard/bids-specification/pull/1539)
+- Permit CITATION.cff as structured alternative to some dataset_description fields [#1525](https://github.com/bids-standard/bids-specification/pull/1525)
+- Add screen parameters metadata [#1369](https://github.com/bids-standard/bids-specification/pull/1369)
Miscellaneous:
-- Clarify meaning of raw vs derivative datasets [#1537](https://github.com/bids-standard/bids-specification/pull/1537)
-- Demote `sample` and `value` columns in `events.tsv` from OPTIONAL to arbitrary [#1457](https://github.com/bids-standard/bids-specification/pull/1457)
+- Clarify meaning of raw vs derivative datasets [#1537](https://github.com/bids-standard/bids-specification/pull/1537)
+- Demote `sample` and `value` columns in `events.tsv` from OPTIONAL to arbitrary [#1457](https://github.com/bids-standard/bids-specification/pull/1457)
[Full release note](https://bids-specification.readthedocs.io/en/latest/CHANGES.html#v190-2023-11-20)
diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md
index e28b0fb7..e2c91fad 100644
--- a/docs/collaboration/governance.md
+++ b/docs/collaboration/governance.md
@@ -2,45 +2,124 @@
## 1. Introduction
-This document, _Brain Imaging Data Structure (BIDS): Governance and Decision Making_, intends to describe the BIDS mission, its principles, its scope, the leadership structure, governance over the standard development process, and to define the different groups and roles. BIDS is a community-built and maintained standard. The goal of this document is to clearly describe how BIDS is maintained and grown.
+This document, *Brain Imaging Data Structure (BIDS): Governance and Decision Making*,
+intends to describe the BIDS mission, its principles,
+its scope, the leadership structure, governance over the standard development process,
+and to define the different groups and roles.
+BIDS is a community-built and maintained standard.
+The goal of this document is to clearly describe how BIDS is maintained and grown.
## 2. Background
### A. Project Summary
-The Brain Imaging Data Structure (BIDS) is a standard specifying the description of neuroimaging data in a filesystem hierarchy and of the metadata associated with the imaging data. The current edition of the standard is available in [HTML][specification] with all the previous editions available since October 2018 (listed in the [Changelog](https://bids-specification.readthedocs.io/en/stable/CHANGES.html)). The pre-October 2018 specification editions can be found in this [repository][bids_wesbite_gh] as PDFs. The development edition is available in [HTML][specification]. The specification is based in a [GitHub repository][specification_gh] and rendered with [ReadTheDocs](https://docs.readthedocs.io/en/stable/).
-
-We strive for community consensus in decision making. This governing model and decision making procedure was developed through the review of several governance models across the informatics and computing field.
-
-The project is a community-driven effort. BIDS, originally OBIDS, was initiated during an INCF sponsored data sharing working group meeting (January 2015) at Stanford University. It was subsequently spearheaded and maintained by Chris Gorgolewski. In the transitional period after Chris Gorgolewski's departure in early 2019 and before the community's acceptance of the present governance in late 2019, the project was managed and maintained by Franklin Feingold, Stefan Appelhoff, and the Poldrack Lab at Stanford. BIDS has advanced under the direction and effort of its contributors, the community of researchers that appreciate the value of standardizing neuroimaging data to facilitate sharing and analysis. The project is multifaceted and depends on contributors for: specification development and maintenance, [BIDS Extension Proposals (BEPs)](../extensions/beps.md), software tools, [starter kits](https://bids-standard.github.io/bids-starter-kit/), [examples][bids_examples_gh], and general discussions. The relevant discussions are located in our [Google Group][bids_google_group], [GitHub organization][bids_standard], and public Google Documents (typically associated with an [extension proposal](../extensions/beps.md)).
-
-A key component of the BIDS initiative is the collection of associated software tools and platforms that facilitate the validation and ease the use of BIDS-formatted datasets. BIDS converters (for example, [HeuDiConv](https://github.com/nipy/heudiconv)) enable the streamlined conversion of raw imaging files (for example, DICOMs) into a BIDS dataset, the [BIDS validator](http://bids-standard.github.io/bids-validator/) allows users to confirm that a given dataset complies with the current edition of the standard, the [PyBIDS](https://github.com/bids-standard/pybids) Python and [bids-matlab](https://github.com/bids-standard/bids-matlab) libraries allow querying and manipulating BIDS-compliant datasets, [BIDS-Apps](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html) for running portable pipelines on validated BIDS datasets, and platforms like [OpenNeuro][openneuro] store and serve BIDS datasets. Note that the associated software does not fall under the same governance structure as BIDS, although the contributor and user base may largely overlap.
+The Brain Imaging Data Structure (BIDS) is a standard specifying the
+description of neuroimaging data in a filesystem hierarchy and of the
+metadata associated with the imaging data.
+The current edition of the standard is available in
+[HTML](https://bids-specification.readthedocs.io/en/stable/) with all
+the previous editions available since October 2018 (listed in the
+[Changelog](https://bids-specification.readthedocs.io/en/stable/CHANGES.html)). The pre-October 2018 specification editions can be found in this [repository](https://github.com/bids-standard/bids-website) as PDFs.
+The development edition is available in
+[HTML](https://bids-specification.readthedocs.io/en/latest/).
+The specification is based in a [GitHub repository](https://github.com/bids-standard/bids-specification)
+and rendered with [ReadTheDocs](https://docs.readthedocs.io/en/stable/).
+
+We strive for community consensus in decision making.
+This governing model and decision making procedure was developed through
+the review of several governance models across the informatics and computing field.
+
+The project is a community-driven effort.
+BIDS, originally OBIDS, was initiated during an INCF sponsored data
+sharing working group meeting (January 2015) at Stanford University.
+It was subsequently spearheaded and maintained by Chris Gorgolewski.
+In the transitional period after Chris Gorgolewski's departure in early 2019
+and before the community's acceptance of the present governance in late 2019,
+the project was managed and maintained by Franklin Feingold, Stefan Appelhoff, and the Poldrack Lab at Stanford.
+BIDS has advanced under the direction and effort of its contributors,
+the community of researchers that appreciate the value of standardizing neuroimaging data to facilitate sharing and analysis.
+The project is multifaceted and depends on contributors for:
+specification development and maintenance,
+[BIDS Extension Proposals (BEPs)](../extensions/beps.md),
+software tools,
+[starter kits](https://bids-standard.github.io/bids-starter-kit/),
+[examples](https://github.com/bids-standard/bids-examples),
+and general discussions.
+The relevant discussions are located in our
+[Google Group](https://groups.google.com/forum/#!forum/bids-discussion),
+[GitHub organization](https://github.com/bids-standard),
+and public Google Documents (typically associated with an [extension proposal](../extensions/beps.md)).
+
+A key component of the BIDS initiative is the collection of associated
+software tools and platforms that facilitate the validation and ease the
+use of BIDS-formatted datasets.
+BIDS converters (for example, [HeuDiConv](https://github.com/nipy/heudiconv)) enable the streamlined
+conversion of raw imaging files (for example, DICOMs) into a BIDS dataset, the
+[BIDS validator](http://bids-standard.github.io/bids-validator/) allows
+users to confirm that a given dataset complies with the current edition
+of the standard, the [PyBIDS](https://github.com/bids-standard/pybids)
+Python and [bids-matlab](https://github.com/bids-standard/bids-matlab)
+libraries allow querying and manipulating BIDS-compliant datasets,
+[BIDS-Apps](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html) for running portable
+pipelines on validated BIDS datasets, and platforms like
+[OpenNeuro](https://openneuro.org/) store and serve BIDS datasets. Note
+that the associated software does not fall under the same governance
+structure as BIDS, although the contributor and user base may largely
+overlap.
### B. BIDS Mission Statement
-The goal of BIDS is to make neuroimaging data more accessible, shareable, and usable by researchers. To achieve this goal, BIDS seeks to develop a simple and intuitive way to organize and describe neuroimaging and associated data. BIDS has three foundational principles:
+The goal of BIDS is to make neuroimaging data more accessible,
+shareable, and usable by researchers. To achieve this goal, BIDS seeks
+to develop a simple and intuitive way to organize and describe
+neuroimaging and associated data. BIDS has three foundational
+principles:
-1. To minimize complexity and facilitate adoption, reuse existing methods and technologies whenever possible.
+1. To minimize complexity and facilitate adoption, reuse existing
+ methods and technologies whenever possible.
-1. Tackle 80% of the most commonly used neuroimaging data, derivatives, and models (inspired by the pareto principle).
+1. Tackle 80% of the most commonly used neuroimaging data, derivatives,
+ and models (inspired by the pareto principle).
-1. Adoption by the global neuroimaging community and their input during the creation of the specification is critical for the success of the project.
+1. Adoption by the global neuroimaging community and their input during
+ the creation of the specification is critical for the success of the project.
## 3. Leadership structure
-To achieve the goals of widespread adoption of the standard while growing to adapt to its community of members, BIDS is led by a series of groups.
+To achieve the goals of widespread adoption of the standard while
+growing to adapt to its community of members, BIDS is led by a series of groups.
-The following figure illustrates the structure of the groups described in this document. The specific organization and responsibilities of these groups are laid out in detail, below.
+The following figure illustrates the structure of the groups described
+in this document. The specific organization and responsibilities of
+these groups are laid out in detail, below.
### BIDS Steering Group
-The BIDS Steering Group is responsible for approving and advancing BEPs through the BIDS standard process, as well as more general decisions regarding the standard. The BIDS Steering Group aims to preserve the longevity and sustainability of the BIDS standard. The BIDS Steering Group consists of 5 members, including the chair.
-
-Membership on the BIDS Steering Group is through elections by BIDS Contributors. BIDS Steering Group terms are 3 years. The existing BIDS Steering Group is responsible for filling open positions, ensuring that at least two nominees are named for each position, that multiple imaging modalities (for example, MRI, MEG) are represented on the final committee, and the different needs for the specification (for example, users vs software developers). Given that the modalities included in BIDS will continue to evolve, we do not recommend a precise mechanism for this balance. It is therefore at the discretion of the Steering Group to ensure that modalities are appropriately represented. The chair is elected by a majority of the BIDS Steering Group (3 votes) to serve for a 1 year term. The chair cannot serve two consecutive years as chair. BIDS Steering Group members may hold other BIDS roles at the same time, for example BEP Working Group chair.
-
-The BIDS Steering Group is the authority of last resort in addressing conflicts among groups and alleged violations of the [Code of Conduct](./bids_github/CODE_OF_CONDUCT.md).
+The BIDS Steering Group is responsible for approving and advancing BEPs
+through the BIDS standard process, as well as more general decisions
+regarding the standard. The BIDS Steering Group aims to preserve the
+longevity and sustainability of the BIDS standard. The BIDS Steering
+Group consists of 5 members, including the chair.
+
+Membership on the BIDS Steering Group is through elections by BIDS
+Contributors. BIDS Steering Group terms are 3 years.
+The existing BIDS Steering Group is responsible for filling open
+positions, ensuring that at least two nominees are named for each
+position, that multiple imaging modalities (for example, MRI, MEG) are
+represented on the final committee, and the different needs for the
+specification (for example, users vs software developers). Given that the
+modalities included in BIDS will continue to evolve, we do not recommend
+a precise mechanism for this balance. It is therefore at the discretion
+of the Steering Group to ensure that modalities are appropriately
+represented. The chair is elected by a majority of the BIDS Steering
+Group (3 votes) to serve for a 1 year term. The chair cannot serve two
+consecutive years as chair. BIDS Steering Group members may hold other
+BIDS roles at the same time, for example BEP Working Group chair.
+
+The BIDS Steering Group is the authority of last resort in addressing
+conflicts among groups and alleged violations of the [Code of Conduct](./bids_github/CODE_OF_CONDUCT.md).
The Steering Group may delegate tasks as needed to fulfill its responsibilities.
@@ -54,17 +133,36 @@ Past members of the Steering group are:
### BEP Working Group
-A BEP Working Group is established for every BIDS Extension Proposal (BEP). Each working group will have 1-3 group-appointed leader(s), referred to as BEP Lead(s). Every BEP Working Group is formed with the aim of extending or modifying the BIDS standard into their domain of interest. This can be either an unspecified modality or derivative. The BEP Lead and Working Group will determine how they organize their work, following the BIDS governance standards laid out in section 4 of this document and the BIDS [Code of Conduct](./bids_github/CODE_OF_CONDUCT.md). The BEP Working Group work is completed when their BEP has become a Merged BEP.
+A BEP Working Group is established for every BIDS Extension Proposal
+(BEP). Each working group will have 1-3 group-appointed leader(s),
+referred to as BEP Lead(s). Every BEP Working Group is formed with the
+aim of extending or modifying the BIDS standard into their domain of
+interest. This can be either an unspecified modality or derivative.
+The BEP Lead and Working Group will determine how they organize their
+work, following the BIDS governance standards laid out in section 4 of
+this document and the BIDS [Code of Conduct](./bids_github/CODE_OF_CONDUCT.md).
+The BEP Working Group work is completed when their BEP has become a Merged BEP.
### BEP Leads Group
-The BEP Leads Group consists of the BEP Leads of the BEP Working Groups. This Working Group intends to ensure potential integrations and collaborations across BEPs are realized and consistency across the BIDS standard.
+The BEP Leads Group consists of the BEP Leads of the BEP Working Groups.
+This Working Group intends to ensure potential integrations and
+collaborations across BEPs are realized and consistency across the BIDS
+standard.
### BIDS Maintainers Group
-This group is responsible for maintaining the [BIDS specification on GitHub][specification_gh]. The Lead Maintainer and the Maintainers Group will determine how they organize their work, detailed in the [BIDS Maintainers guide](https://docs.google.com/document/d/11U43QmYVZUVdCxpJeezmYpkHf4sbzWjjN2EIjbk4Pfo/edit) and in accordance with the BIDS Code of Conduct. The maintainers guide is subject to Steering Group approval and amendment. BIDS contributors may self-nominate to become maintainers, with approval by a majority vote of current maintainers.
+This group is responsible for maintaining the [BIDS specification on
+GitHub](https://github.com/bids-standard/bids-specification). The Lead
+Maintainer and the Maintainers Group will determine how they organize
+their work, detailed in the [BIDS Maintainers guide](https://docs.google.com/document/d/11U43QmYVZUVdCxpJeezmYpkHf4sbzWjjN2EIjbk4Pfo/edit) and in accordance with the BIDS Code of Conduct.
+The maintainers guide is subject to Steering Group approval and amendment.
+BIDS contributors may self-nominate to become maintainers,
+with approval by a majority vote of current maintainers.
-This group submits [monthly status summaries](https://github.com/bids-standard/bids-specification/wiki/BIDS-Maintainers-Documents#bids-maintainers-reports) to the Steering Group.
+This group submits
+[monthly status summaries](https://github.com/bids-standard/bids-specification/wiki/BIDS-Maintainers-Documents#bids-maintainers-reports)
+to the Steering Group.
The current members of the Maintainers group are:
@@ -74,61 +172,105 @@ Past members of the Maintainers group are:
{{ MACROS___generate_members_table(file="past_maintainers.yml") }}
-If you need to contact the maintainers on a specific topic you can use the following email: `bids.maintenance@gmail.com`. However, you may receive a more timely response when pinging them on one of the GitHub repositories using the tag `@bids-standard/maintainers`.
+If you need to contact the maintainers on a specific topic you can use the following email: `bids.maintenance@gmail.com`.
+However, you may receive a more timely response when pinging them on one of the GitHub repositories using the tag `@bids-standard/maintainers`.
### BIDS Contributors Group
-This group consists of individuals who have contributed to the BIDS community. Group members are identified on the [BIDS contributors](https://bids-specification.readthedocs.io/en/latest/appendices/contributors.html) list, a list that is intended to be inclusive of all forms of engagement with the BIDS community, and that contributors are encouraged to update via the [specification wiki](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors). Engagement can range from writing copy text in the specification to providing feedback on projects such as the [BIDS starter kit](https://bids-standard.github.io/bids-starter-kit/).
-
-Members of the BIDS Contributors Group are encouraged to support the BIDS specification by supporting the members of the Maintainers Group in their responsibilities.
-
-An _Active Contributor_ is defined as a contributor that is reachable via the email address they provided to the BIDS Maintainers team, and responds to correspondence by the BIDS group (for example, Maintainers/Steering Group or the BIDS community at large). Contributors may explicitly opt in or out of activity at any time. The Maintainers Group is responsible for providing transparent procedures for contributors to opt in/out as well as providing procedures for removing non-responsive members from the list of active contributors. In case of no response, a grace period of two years is in place before a formerly active contributor loses their "active" status.
+This group consists of individuals who have contributed to the BIDS
+community. Group members are identified on the [BIDS
+contributors](https://bids-specification.readthedocs.io/en/latest/99-appendices/01-contributors.html) list,
+a list that is intended to be inclusive of all forms of engagement with the BIDS community,
+and that contributors are encouraged to update via the
+[specification wiki](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors).
+Engagement can range from writing copy text in the specification
+to providing feedback on projects such as the
+[BIDS starter kit](https://bids-standard.github.io/bids-starter-kit/).
+
+Members of the BIDS Contributors Group are encouraged to support the
+BIDS specification by supporting the members of the Maintainers Group in
+their responsibilities.
+
+An *Active Contributor* is defined as a contributor that is reachable via
+the email address they provided to the BIDS Maintainers team,
+and responds to correspondence by the BIDS group
+(for example, Maintainers/Steering Group or the BIDS community at large).
+Contributors may explicitly opt in or out of activity at any time.
+The Maintainers Group is responsible for providing transparent procedures for
+contributors to opt in/out as well as providing procedures for
+removing non-responsive members from the list of active contributors.
+In case of no response,
+a grace period of two years is in place before a formerly active contributor
+loses their "active" status.
### BIDS Advisory Group
-The purpose of this group is to provide advice and guidance to the BIDS Steering Group and the BEP Leads Group. When a BEP is merged into the specification, the leads of this BEP working group automatically join the advisory group. Members are encouraged to participate for at least 2 years following the merge of their BEP. If an advisory group member decides to leave the advisory group, they should inform the steering group in advance and are responsible to help:
+The purpose of this group is to provide advice and guidance to the BIDS Steering
+Group and the BEP Leads Group.
+When a BEP is merged into the specification,
+the leads of this BEP working group automatically join the advisory group.
+Members are encouraged to participate for at least 2 years following
+the merge of their BEP.
+If an advisory group member decides to leave the advisory group,
+they should inform the steering group in advance and are responsible to help:
-- provide a list of possible replacement candidates from the BIDS community with a similar level of expertise to theirs, and
+- provide a list of possible replacement candidates from the BIDS community
+ with a similar level of expertise to theirs, and
-- assist the steering and maintainers in choosing a suitable replacement.
+- assist the steering and maintainers in choosing a suitable replacement.
{{ MACROS___generate_members_table(file="advisory.yml") }}
### Other working groups
-A working/interest group can be established under the approval of the BIDS Steering Group. This is typically but not limited to being formed for the purpose of advancing the BIDS community, not the standard.
+A working/interest group can be established under the approval of the BIDS Steering Group.
+This is typically but not limited to being formed for the purpose of advancing the BIDS community, not the standard.
-Each group will appoint 1-2 chairs. Members of these groups can have cross appointments in other groups (for example, BEP Working Group). These groups do not necessarily dissolve after some duration or event, unless stated in their proposal.
+Each group will appoint 1-2 chairs.
+Members of these groups can have cross appointments in other groups (for example, BEP Working Group).
+These groups do not necessarily dissolve after some duration or event, unless stated in their proposal.
-The working/interest group formation is formalized through an open letter via a "read-only" Google Document addressed to the BIDS Steering Group. The open letter will be posted on:
+The working/interest group formation is formalized
+through an open letter via a "read-only" Google Document addressed to the BIDS Steering Group.
+The open letter will be posted on:
-- the [BIDS-Specification GitHub repository][specification_gh],
-- [Google Group][bids_google_group],
-- and [social media channels](https://github.com/bids-standard/bids-specification?tab=readme-ov-file#BIDS-communication-channels).
+- the [BIDS-Specification GitHub repository](https://github.com/bids-standard/bids-specification),
+- [Google Group](https://groups.google.com/forum/#!forum/bids-discussion),
+- and [social media channels](