diff --git a/.circleci/config.yml b/.circleci/config.yml
index b3923f164a..b8aa208d9b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -25,3 +25,121 @@ jobs:
command: pipenv run mkdocs build --clean --strict --verbose
- store_artifacts:
path: site
+
+# Auto changelog collector
+ github-changelog-generator:
+ working_directory: ~/build
+ docker:
+ - image: ferrarimarco/github-changelog-generator:1.14.3
+ steps:
+ - setup_remote_docker:
+ version: 17.11.0-ce
+ - checkout
+ - run:
+ name: Build changelog
+ working_directory: ~/build
+ command: |
+ if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
+ github_changelog_generator --user bids-standard --project bids-specification --token ${CHANGE_TOKEN} --output ~/build/CHANGES.md --base ~/build/src/pregh-changes.md --header-label Changelog --no-issues --no-issues-wo-labels --no-filter-by-milestone --no-compare-link --pr-label ""
+ cat ~/build/CHANGES.md
+ mv ~/build/CHANGES.md ~/build/src/CHANGES.md
+ else
+ echo "Commit or Release, do nothing"
+ fi
+ - persist_to_workspace:
+ root: .
+ paths: src
+
+# Clear remark test
+ remark:
+ working_directory: ~
+ docker:
+ - image: node:latest
+ steps:
+ - checkout
+ - attach_workspace:
+ at: ~/build
+ - run:
+ name: update-npm
+ command: |
+ cd ~
+ npm install npm@latest
+ - run:
+ name: get remark
+ command: |
+ cd ~
+ npm install remark remark-cli
+ - run:
+ name: get remark styles
+ command: |
+ cd ~
+ npm install remark-cli@5.0.0 remark-lint@6.0.2 remark-preset-lint-recommended@3.0.2 remark-preset-lint-markdown-style-guide@2.1.2
+ - run: # remark the auto generated changes.md
+ name: remark on autogenerated CHANGES.md
+ command: |
+ cd ~/project
+ if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
+ mkdir ~/project/src/tmp
+ cat ~/build/src/CHANGES.md
+ cp ~/build/src/CHANGES.md ~/project/src/CHANGES.md
+ ~/node_modules/.bin/remark ~/project/src/CHANGES.md -o ~/project/src/tmp/CHANGES.md
+ ~/node_modules/.bin/remark ~/project/src/tmp/CHANGES.md --frail
+ else
+ echo "Commit or Release, do nothing"
+ mkdir ~/project/src/tmp
+ touch ~/project/src/tmp/empty.txt
+ fi
+ - persist_to_workspace:
+ root: ~/project/src
+ paths: tmp
+
+# Push built changelog to repo
+ Changelog-bot:
+ working_directory: ~/build
+ docker:
+ - image: circleci/openjdk:8-jdk
+ steps:
+ - setup_remote_docker:
+ version: 17.11.0-ce
+ - checkout
+ - attach_workspace:
+ at: ~/build
+ - deploy:
+ name: Changelog deployment
+ working_directory: ~/build
+ command: |
+ if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
+ mv ~/build/tmp/CHANGES.md ~/build/src/CHANGES.md
+ merge_messsge=$(git log -1 | grep Merge | grep "pull")
+ PR_number=$(echo $merge_messsge | cut -d ' ' -f 4)
+ git config credential.helper 'cache --timeout=120'
+ git config user.email "franklin.feingold@gmail.com"
+ git config user.name "Changelog-bot"
+ git add ~/build/src/CHANGES.md
+ git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
+ git push https://${CHANGE_TOKEN}@github.com/bids-standard/bids-specification.git master
+ else
+ echo "Commit or Release, do nothing"
+ fi
+
+workflows:
+ version: 2
+ search_build:
+ jobs:
+ - build
+ - github-changelog-generator:
+ filters:
+ branches:
+ only: master
+ - remark:
+ requires:
+ - github-changelog-generator
+ filters:
+ branches:
+ only: master
+ - Changelog-bot:
+ requires:
+ - remark
+ filters:
+ branches:
+ only: master
diff --git a/.remarkrc b/.remarkrc
index a11579d913..2031e350e3 100644
--- a/.remarkrc
+++ b/.remarkrc
@@ -1,6 +1,9 @@
{
"plugins": [
"preset-lint-markdown-style-guide",
- ["lint-no-duplicate-headings", false]
+ ["lint-no-duplicate-headings", false],
+ ["lint-list-item-indent", "tab-size"],
+ ["lint-emphasis-marker", "consistent"],
+ ["lint-maximum-line-length", false]
]
}
diff --git a/CODEOWNERS b/CODEOWNERS
new file mode 100644
index 0000000000..c245f8bebc
--- /dev/null
+++ b/CODEOWNERS
@@ -0,0 +1,16 @@
+# This files DOES NOT list people responsible for maintenance of different parts of
+# the specification. It merely serves the purpose of notifying interested
+# contributors when a new Pull Request that proposes changes to a particular file
+# is submitted. If you would like to subscribe to such notifications (in a form of a
+# Request for Review) please add your GitHub username next to the file you want to
+# monitor below.
+
+# Add your GitHub name below to get notified about proposed releases
+/src/CHANGES.md @chrisgorgo @sappelhoff @CPernet
+
+# Individual sections
+/src/01-common-principles.md @chrisgorgo @DimitriPapadopoulos
+/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @chrisgorgo
+/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff @ezemikulan
+/src/04-modality-specific-files/04-intracranial-electroencephalography.md @ezemikulan
+/src/99-appendices/06-meg-file-formats.md @monkeyman192
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 314170e2fa..07ebbc74dd 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -44,9 +44,9 @@ The specification documents follow the [Markdown Style Guide](http://www.cirosan
You
can validate your changes against the guide using [remark](https://github.com/remarkjs/remark-lint) which works as a
[standalone command line tool](https://github.com/remarkjs/remark/tree/master/packages/remark-cli) as well as [a plugin for various text editors](https://github.com/remarkjs/remark-lint#editor-integrations). Remark preserves consistent markdown styling across the contributions. Please ensure before submitting a contribution that you do not have any linter errors in your text editor.
-You can also use [prettier](https://github.com/prettier/prettier) to automatically correct some of the style issuse that might be found in the proposed changes.
+You can also use [prettier](https://github.com/prettier/prettier) to automatically correct some of the style issues that might be found in the proposed changes.
-We have deployed a continous integrator ([circle CI](https://circleci.com/)) to further allow for integrating changes continously. The CI is testing that the changes are inline with our standard styling.
+We have deployed a continuous integrator ([circle CI](https://circleci.com/)) to further allow for integrating changes continuously. The CI is testing that the changes are inline with our standard styling.
GitHub has a helpful page on [getting started with writing and formatting on GitHub](https://help.github.com/articles/getting-started-with-writing-and-formatting-on-github).
@@ -95,9 +95,25 @@ Try to keep the changes focused. If you submit a large amount of work in all in
#### 4. Submit a [pull request](https://help.github.com/articles/about-pull-requests/)
+Please keep the title of your pull request short but informative - it will
+appear in the [changelog](src/CHANGES.md).
+
+Use one of the following prefixes in the title of your pull request:
+ - `[ENH]` - enhancement of the specification that adds a new feature or
+ support for a new data type
+ - `[FIX]` - fix of a typo or language clarification
+ - `[INFRA]` - changes to the infrastructure automating the specification
+ release (for example building HTML docs etc.)
+ - `[MISC]` - everything else including changes to the file listing
+ contributors
+
+If you are opening a pull request to obtain early feedback, but the changes
+are not ready to be merged (a.k.a. Work in Progress pull request) please
+use a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
+
A member of the BIDS Specification team will review your changes to confirm that they can be merged into the main codebase.
-A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your github notifications and be prepared to join in that conversation.
+A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your GitHub notifications and be prepared to join in that conversation.
You can update your [fork](https://help.github.com/articles/about-forks/) of the BIDS Specification and the pull request will automatically update with those commits. You don't need to submit a new pull request when you make a change in response to a review.
@@ -110,6 +126,10 @@ GitHub has a [nice introduction](https://help.github.com/articles/github-flow/)
` branch based on
+`upstream/master`.
+For example, if releasing version `1.2.0`:
+
+```Shell
+$ git fetch upstream
+$ git checkout -b rel/1.2.0 upstream/master
+```
+
+### 2. Update the version in the changelog and mkdocs.yml
+
+Change the "Unreleased" heading in
+[src/CHANGES.md](https://github.com/bids-standard/bids-specification/blob/master/src/CHANGES.md)
+to `v`, and link to the target ReadTheDocs URL.
+If the target release date is known, include the date in YYYY-MM-DD in parentheses after
+the link.
+
+```Diff
+- ## Unreleased
++ ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) (2019-03-04)
+```
+
+The date can be changed or added later, so accurate prediction is not necessary.
+
+Remove the `-dev` from the version in
+[mkdocs.yml](https://github.com/bids-standard/bids-specification/blob/master/mkdocs.yml)
+configuration, so the title will be correct for the released specification.
+If the version preceding the `-dev` is not the target version, update the version as well.
+In the figure below, we update `v1.2.0-dev` to `v1.2.0`.
+
+
+### 3. Commit changes and push to upstream
+
+By pushing `rel/` branches to the main repository, the chances of continuous integration
+discrepancies is reduced.
+
+```Shell
+$ git add src/CHANGES.md mkdocs.yml
+$ git commit -m 'REL: v1.2.0`
+$ git push -u upstream rel/1.2.0
+```
+
+### 4. Open a pull request against the master branch
+Important note: The pull request title **must** be named "REL: vX.Y.Z" (*e.g.*, "REL: v1.2.0").
+
+**This will open a period of discussion for 5 business days regarding if we are ready to release.**
+
+Minor revisions may be made using GitHub's [suggestion
+feature](https://help.github.com/en/articles/incorporating-feedback-in-your-pull-request).
+For larger changes, pull requests should be made against `master`.
+
+**Merging other pull requests during this period requires agreement in this discussion.**
+
+There are no hard-and-fast rules for what other pull requests might be merged, but the focus
+should generally be on achieving a self-consistent, backwards-compatible document.
+For example, if an inconsistency is noticed, a PR might be necessary to resolve it.
+Merging an entire BEP would likely lead to greater uncertainty about self-consistency, and should
+probably wait.
+
+If `master` is updated, it should be merged into the `rel/` branch:
+
+```Shell
+$ get fetch upstream
+$ git checkout rel/1.2.0
+$ git merge upstream/master
+$ git push rel/1.2.0
+```
+
+### 5. Clean the changelog
+
+Review `src/CHANGES.md` to ensure that the document produces a changelog that is useful to a
+reader of the specification.
+For example, several small PRs fixing typos might be merged into a single line-item, or less
+important changes might be moved down the list to ensure that large changes are more prominent.
+
+### 6. Set release date and merge
+
+On the day of release, the current date should be added to/updated in the changelog in the form
+YYYY-MM-DD.
+The date should be placed after the link to the versioned URL.
+For example:
+
+```Diff
+- ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/)
++ ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) (2019-03-04)
+```
+
+Verify that the pull request title matches "REL: vX.Y.Z" and merge the pull request.
+
+### 7. Tag the release
+
+GitHub's release mechanism does not have all of the features we need, so manually tag the release
+in your local repository.
+To do this, `fetch` the current state of `upstream` (see step 1), tag `upstream/master`, and
+`push` the tag to `upstream`.
+
+```Shell
+$ git fetch upstream
+$ git tag -a -m "v1.2.0 (2019-03-04)" v1.2.0 upstream/master
+$ git push upstream v1.2.0
+```
+
+There are four components to the tag command:
+
+1. `-a-` indicates that we want to use an
+ [annotated tag](https://git-scm.com/book/en/v2/Git-Basics-Tagging#_creating_tags), which will
+ ensure that [`git describe`](https://git-scm.com/docs/git-describe) works nicely with the
+ repository.
+2. `-m ` is the message that will be saved with the tag.
+3. `v` is the name of the release and the tag.
+4. `upstream/master` instructs `git` to tag the most recent commit on the `master` branch of the
+ `upstream` remote.
+
+### 8. Create a GitHub release
+
+Some GitHub processes may only trigger on a GitHub release, rather than a tag push.
+To make a GitHub release, go to the [Releases
+](https://github.com/bids-standard/bids-specification/releases) page:
+
+
+Click [Draft a new release](https://github.com/bids-standard/bids-specification/releases/new):
+
+
+
+Set the tag version and release title to "vX.Y.Z", and paste the current changelog as the
+description:
+
+
+
+Click "Publish release".
+
+### 9. Edit the mkdocs.yml file site_name to set a new development version
+
+Please submit a PR with the title `REL: -dev`.
+This should be the first merged PR in the new version.
+This process is illustrated below.
+
+
+
+Note that the development version number should be larger than the last release, with the
+version of the next *intended* release, followed by `-dev`.
+For example, after the 1.3.0 release, either `1.3.1-dev` or `1.4.0-dev` would be reasonable, based
+on the expected next version.
diff --git a/Whitelogo_transparent-background.png b/Whitelogo_transparent-background.png
new file mode 100644
index 0000000000..deb07b6449
Binary files /dev/null and b/Whitelogo_transparent-background.png differ
diff --git a/mkdocs.yml b/mkdocs.yml
index a6149e3786..7de77b24f1 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,5 +1,10 @@
-site_name: Brain Imaging Data Structure
+site_name: Brain Imaging Data Structure v1.3.0-dev
theme: material
+extra_javascript:
+ - js/jquery-3.4.1.min.js
+markdown_extensions:
+ - toc:
+ anchorlink: true
plugins:
- search
docs_dir: 'src'
@@ -12,9 +17,11 @@ nav:
- Modality specific files:
- Magnetic Resonance Imaging: 04-modality-specific-files/01-magnetic-resonance-imaging-data.md
- Magnetoencephalography: 04-modality-specific-files/02-magnetoencephalography.md
- - Task events: 04-modality-specific-files/03-task-events.md
- - Physiological and other continous recordings: 04-modality-specific-files/04-physiological-and-other-continous-recordings.md
- - Behavioral experiments (with no MRI): 04-modality-specific-files/05-behavioural-experiments.md
+ - Electroencephalography: 04-modality-specific-files/03-electroencephalography.md
+ - intracranial Electroencephalography: 04-modality-specific-files/04-intracranial-electroencephalography.md
+ - Task events: 04-modality-specific-files/05-task-events.md
+ - Physiological and other continuous recordings: 04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
+ - Behavioral experiments (with no MRI): 04-modality-specific-files/07-behavioral-experiments.md
- Longitudinal and multi-site studies: 05-longitudinal-and-multi-site-studies.md
- Extending the BIDS specification: 06-extensions.md
- Appendix:
@@ -26,4 +33,5 @@ nav:
- MEG file formats: 99-appendices/06-meg-file-formats.md
- MEG systems: 99-appendices/07-meg-systems.md
- Coordinate-systems: 99-appendices/08-coordinate-systems.md
+ - Changelog: CHANGES.md
- The BIDS Starter Kit: https://github.com/bids-standard/bids-starter-kit
diff --git a/pull_request_template.md b/pull_request_template.md
new file mode 100644
index 0000000000..7f01ddbc69
--- /dev/null
+++ b/pull_request_template.md
@@ -0,0 +1,17 @@
+--- PLEASE READ AND DELETE THE TEXT BELOW BEFORE OPENING THE PULL REQUEST ---
+
+- Please keep the title of your pull request short but informative - it will
+ appear in the changelog
+- Use one of the following prefixes in the title of your pull request:
+ - `[ENH]` - enhancement of the specification that adds a new feature or
+ support for a new data type
+ - `[FIX]` - fix of a typo or language clarification
+ - `[INFRA]` - changes to the infrastructure automating the specification
+ release (for example building HTML docs etc.)
+ - `[MISC]` - everything else including changes to the file listing
+ contributors
+- If you are opening a pull request to obtain early feedback, but the changes
+ are not ready to be merged (a.k.a. Work in Progress pull request) please
+ use a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/)
+
+--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---
diff --git a/readthedocs.yml b/readthedocs.yml
index d53ffa68b8..59d9418a9e 100644
--- a/readthedocs.yml
+++ b/readthedocs.yml
@@ -1,5 +1,15 @@
+version: 2
+
+formats: all
+
build:
image: latest
python:
version: 3.6
+ install:
+ - requirements: requirements.txt
+
+mkdocs:
+ configuration: mkdocs.yml
+ fail_on_warning: true
diff --git a/release_images/GH-release_1.png b/release_images/GH-release_1.png
new file mode 100644
index 0000000000..e9222cb07f
Binary files /dev/null and b/release_images/GH-release_1.png differ
diff --git a/release_images/GH-release_2.png b/release_images/GH-release_2.png
new file mode 100644
index 0000000000..4ff4cd4813
Binary files /dev/null and b/release_images/GH-release_2.png differ
diff --git a/release_images/GH-release_3.png b/release_images/GH-release_3.png
new file mode 100644
index 0000000000..224bcea291
Binary files /dev/null and b/release_images/GH-release_3.png differ
diff --git a/release_images/Unreleased-to-Version.png b/release_images/Unreleased-to-Version.png
new file mode 100644
index 0000000000..74bf6fb9d2
Binary files /dev/null and b/release_images/Unreleased-to-Version.png differ
diff --git a/release_images/site_name_2dev-3.png b/release_images/site_name_2dev-3.png
new file mode 100644
index 0000000000..1f8d48bbb7
Binary files /dev/null and b/release_images/site_name_2dev-3.png differ
diff --git a/release_images/site_name_3-3dev.png b/release_images/site_name_3-3dev.png
new file mode 100644
index 0000000000..5069501185
Binary files /dev/null and b/release_images/site_name_3-3dev.png differ
diff --git a/release_images/site_name_release_1.2-1.3dev.png b/release_images/site_name_release_1.2-1.3dev.png
new file mode 100644
index 0000000000..6eeca8b670
Binary files /dev/null and b/release_images/site_name_release_1.2-1.3dev.png differ
diff --git a/release_images/site_name_release_1.2dev-1.2.png b/release_images/site_name_release_1.2dev-1.2.png
new file mode 100644
index 0000000000..b6be452d97
Binary files /dev/null and b/release_images/site_name_release_1.2dev-1.2.png differ
diff --git a/src/01-introduction.md b/src/01-introduction.md
index fbf0e68cc4..fe0f66b676 100644
--- a/src/01-introduction.md
+++ b/src/01-introduction.md
@@ -8,7 +8,7 @@ obtained in neuroimaging experiments. Even two researchers working in the same
lab can opt to arrange their data in a different way. Lack of consensus (or a
standard) leads to misunderstandings and time wasted on rearranging data or
rewriting scripts expecting certain structure. Here we describe a simple and
-easy-to-adopt way of organising neuroimaging and behavioural data. By using this
+easy-to-adopt way of organising neuroimaging and behavioral data. 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
@@ -45,7 +45,7 @@ different backgrounds.
## Extensions
The BIDS specification can be extended in a backwards compatible way and will
-evolve over time. This is accomplished through community-driven BIDS Extention
+evolve over time. This is accomplished through community-driven BIDS Extension
Proposals (BEPs). For more information about the BEP process, and list of
current BEP proposals, see
[Extending the BIDS specification](06-extensions.md).
diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 4ff12e996a..0d15b1e80b 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -6,16 +6,16 @@ The keywords "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD",
"SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be
interpreted as described in [[RFC2119](https://www.ietf.org/rfc/rfc2119.txt)].
-Throughout this protocol we use a list of terms. To avoid misunderstanding we
-clarify them here.
+Throughout this specification we use a list of terms. To avoid
+misunderstanding we clarify them here.
-1. Dataset - a set of neuroimaging and behavioural data acquired for a purpose
+1. Dataset - a set of neuroimaging and behavioral data acquired for a purpose
of a particular study. A dataset consists of data acquired from one or more
subjects, possibly from multiple sessions.
1. Subject - a person or animal participating in the study.
-1. Session - a logical grouping of neuroimaging and behavioural data consistent
+1. Session - a logical grouping of neuroimaging and behavioral data consistent
across subjects. Session can (but doesn't have to) be synonymous to a visit
in a longitudinal study. In general, subjects will stay in the scanner
during one session. However, for example, if a subject has to leave the
@@ -33,17 +33,17 @@ clarify them here.
scanning sequence/protocol.
1. Data type - a functional group of different types of data. In BIDS we define
- five data types: func (task based and resting state functional MRI), dwi
+ six data types: func (task based and resting state functional MRI), dwi
(diffusion weighted imaging), fmap (field inhomogeneity mapping data such as
field maps), anat (structural imaging such as T1, T2, etc.), meg
- (magnetoencephalography).
+ (magnetoencephalography), beh (behavioral).
1. Task - a set of structured activities performed by the participant. Tasks
are usually accompanied by stimuli and responses, and can greatly vary in
- complexity. For the purpose of this protocol we consider the so-called
+ complexity. For the purpose of this specification we consider the so-called
“resting state” a task. In the context of brain scanning, a task is always
tied to one data acquisition. Therefore, even if during one acquisition the
- subject performed multiple conceptually different behaviours (with different
+ subject performed multiple conceptually different behaviors (with different
sets of instructions) they will be considered one (combined) task.
1. Event - a stimulus or subject response recorded during a task. Each event
@@ -109,6 +109,29 @@ these data are to be included:
1. We RECOMMEND including the PDF print-out with the actual sequence parameters
generated by the scanner in the `sourcedata` folder.
+Alternatively one can organize their data in the following way
+
+```Text
+my_dataset/
+ sourcedata/
+ ...
+ rawdata/
+ dataset_description.json
+ participants.tsv
+ sub-01/
+ sub-02/
+ ...
+ derivatives/
+ ...
+```
+
+In this example **only the `rawdata` subfolder needs to be BIDS compliant**
+dataset. This specification does not prescribe anything about the contents of
+`sourcedata` and `derivatives` folders in the above example - nor does it
+prescribe the `sourcedata`, `derivatives`, or `rawdata` folder names. The above
+example is just a convention that can be useful for organizing raw, source, and
+derived data while maintaining BIDS compliancy of the raw data folder.
+
## The Inheritance Principle
Any metadata file (`.json`, `.bvec`, `.tsv`, etc.) may be defined at any
@@ -128,13 +151,13 @@ participant can exist only at participant level directory, i.e
specific to a participant is to be declared only at top level of dataset for eg:
`task-sist_bold.json` must be placed under `/dataset/task-sist_bold.json`
-Example 1: Two JSON files at same level that are applicable for NIfTI file.
+Example 1: Two JSON files that are erroneously at the same level.
```Text
sub-01/
ses-test/
- sub-test_task-overtverbgeneration_bold.json
- sub-test_task-overtverbgeneration_run-2_bold.json
+ sub-01_ses-test_task-overtverbgeneration_bold.json
+ sub-01_ses-test_task-overtverbgeneration_run-2_bold.json
anat/
sub-01_ses-test_T1w.nii.gz
func/
@@ -146,8 +169,8 @@ In the above example, two JSON files are listed under `sub-01/ses-test/`, which
are each applicable to
`sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz`, violating the
constraint that no more than one file may be defined at a given level of the
-directory structure. Instead `task-overtverbgeneration_run-2_bold.json` should
-have been under `sub-01/ses-test/func/`.
+directory structure. Instead `sub-01_ses-test_task-overtverbgeneration_run-2_bold.json`
+should have been under `sub-01/ses-test/func/`.
Example 2: Multiple run and rec with same acquisition (acq) parameters acq-test1
@@ -168,23 +191,30 @@ apply to different runs and rec files. Also if the JSON file
(`task-xyz_acq-test1_bold.json`) is defined at dataset top level directory, it
will be applicable to all task runs with `test1` acquisition parameter.
-Case 2: Multiple json files at different levels for same task and acquisition
-parameters
+Example 3: Multiple json files at different levels for same task and
+acquisition parameters
```Text
+task-xyz_acq-test1_bold.json
sub-01/
- sub-01_task-xyz_acq-test1_bold.json
- anat/
- func/
- sub-01_task-xyz_acq-test1_run-1_bold.nii.gz
- sub-01_task-xyz_acq-test1_rec-recon1_bold.nii.gz
- sub-01_task-xyz_acq-test1_rec-recon2_bold.nii.gz
+ anat/
+ func/
+ sub-01_task-xyz_acq-test1_run-1_bold.nii.gz
+ sub-01_task-xyz_acq-test1_rec-recon1_bold.nii.gz
+ sub-01_task-xyz_acq-test1_rec-recon2_bold.nii.gz
+ sub-01_task-xyz_acq-test1_bold.json
```
-In the above example, the fields from `task-xyz_acq-test1_bold.json` file will
-apply to all bold runs. However, if there is a key with different value in
-`sub-01/func/sub-01_task-xyz_acq-test1_run-1_bold.json`, the new value will be
-applicable for that particular run/task NIfTI file/s.
+In the above example, the fields from the `task-xyz_acq-test1_bold.json` file
+at the top directory will apply to all bold runs. However, if there is a key
+with different value in the
+`sub-01/func/sub-01_task-xyz_acq-test1_run-1_bold.json` file defined at a
+deeper level, that value will be applicable for that particular run/task NIfTI
+file/s. In other words, the `json` file at the deeper level overrides values
+that are potentially also defined in the `.json` at a more shallow level. If the
+`.json` file at the more shallow level contains key-value-pairs that are not
+present in the `.json` file at the deeper level, these key-value-pairs are
+inherited by the `.json` file at the deeper level (but NOT vice versa!).
### Good practice recommendations
@@ -206,24 +236,25 @@ possible. Since the NIfTI standard offers limited support for the various image
acquisition parameters available in DICOM files, we RECOMMEND that users provide
additional meta information extracted from DICOM files in a sidecar JSON file
(with the same filename as the `.nii[.gz]` file, but with a `.json` extension).
-Extraction of BIDS compatible metadata can be performed using dcm2nii
-[https://www.nitrc.org/projects/dcm2nii/](https://www.nitrc.org/projects/dcm2nii/)
-and dicm2nii
-[http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m)
+Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix)
+and [dicm2nii](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m)
DICOM to NIfTI converters. A provided
-validator[https://github.com/INCF/bids-validator](https://github.com/INCF/bids-validator)
+[validator](https://github.com/bids-standard/bids-validator)
will check for conflicts between the JSON file and the data recorded in the
NIfTI header.
### Tabular files
-Tabular data MUST be saved as tab delimited values (`.tsv`) files, i.e. csv
+Tabular data MUST be saved as tab delimited values (`.tsv`) files, i.e., csv
files where commas are replaced by tabs. Tabs MUST be true tab characters and
MUST NOT be a series of space characters. Each TSV file MUST start with a header
line listing the names of all columns (with the exception of physiological and
other continuous acquisition data - see below for details). Names MUST be
separated with tabs. String values containing tabs MUST be escaped using double
-quotes. Missing and non-applicable values MUST be coded as `n/a`.
+quotes. Missing and non-applicable values MUST be coded as `n/a`. Numerical
+values MUST employ the dot (`.`) as decimal separator and MAY be specified
+in scientific notation, using `e` or `E` to separate the significand from the
+exponent. TSV files MUST be in UTF-8 encoding.
Example:
@@ -234,8 +265,13 @@ onset duration response_time correct stop_trial go_trial
Tabular files MAY be optionally accompanied by a simple data dictionary in a
JSON format (see below). The data dictionaries MUST have the same name as their
-corresponding tabular files but with `.json` extensions. Each entry in the data
-dictionary has a name corresponding to a column name and the following fields:
+corresponding tabular files but with `.json` extensions. If a JSON file
+is provided, it MAY contain one or more fields describing the columns found in
+the TSV file (in addition to any other metadata one wishes to include that
+describe the file as a whole). Note that if a field name included in the JSON
+sidecar matches a column name in the TSV file, then that field MUST contain a
+description of the corresponding column, using an object containing the following
+fields:
| Field name | Definition |
| :---------- | :--------------------------------------------------------------------------------------------------------------------- |
@@ -270,12 +306,11 @@ Example:
## Key/value files (dictionaries)
JavaScript Object Notation (JSON) files MUST be used for storing key/value
-pairs. Extensive documentation of the format can be found here:
-[http://json.org/](http://json.org/). Several editors have built-in support for
-JSON syntax highlighting that aids manual creation of such files. An online
-editor for JSON with built-in validation is available at:
-[http://jsoneditoronline.org](http://jsoneditoronline.org). JSON files MUST be
-in UTF-8 encoding.
+pairs. JSON files MUST be in UTF-8 encoding. Extensive documentation of the
+format can be found here: [http://json.org/](http://json.org/). Several editors
+have built-in support for JSON syntax highlighting that aids manual creation of
+such files. An online editor for JSON with built-in validation is available at:
+[http://jsoneditoronline.org](http://jsoneditoronline.org).
Example:
@@ -305,7 +340,7 @@ as SI, from the French Système international (d'unités)) and can be SI units o
SI derived units. In case there are valid reasons to deviate from SI units or SI
derived units, the units MUST be specified in the sidecar JSON file. In case
data is expressed in SI units or SI derived units, the units MAY be specified in
-the sidecar JSON file. In case prefixes are added to SI or non-SI units (e.g.
+the sidecar JSON file. In case prefixes are added to SI or non-SI units (e.g.,
mm), the prefixed units MUST be specified in the JSON file (see [Appendix V](99-appendices/05-units.md):
Units). In particular:
@@ -367,13 +402,13 @@ sub-control01/
sub-control01_magnitude1.nii.gz
sub-control01_scans.tsv
- code/
- deface.py
- derivatives/
- README
- participants.tsv
- dataset_description.json
- CHANGES
+code/
+ deface.py
+derivatives/
+README
+participants.tsv
+dataset_description.json
+CHANGES
```
Additional files and folders containing raw data may be added as needed for
diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 6e13ae2606..731a0c7540 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -49,7 +49,8 @@ Example:
### `README`
In addition a free form text file (`README`) describing the dataset in more
-details SHOULD be provided.
+details SHOULD be provided. The `README` file MUST be either in ASCII or UTF-8
+encoding.
### `CHANGES`
@@ -57,7 +58,7 @@ Version history of the dataset (describing changes, updates and corrections) MAY
be provided in the form of a `CHANGES` text file. This file MUST follow the CPAN
Changelog convention:
[http://search.cpan.org/~haarg/CPAN-Changes-0.400002/lib/CPAN/Changes/Spec.pod](https://metacpan.org/pod/release/HAARG/CPAN-Changes-0.400002/lib/CPAN/Changes/Spec.pod).
-`README` and `CHANGES` files MUST be either in ASCII or UTF-8 encoding.
+The `CHANGES` file MUST be either in ASCII or UTF-8 encoding.
Example:
@@ -173,7 +174,7 @@ decreased. Dates that are shifted for anonymization purposes should be set to a
year 1900 or earlier to clearly distinguish them from unmodified data. Shifting
dates is recommended, but not required.
-Additional fields can include external behavioural measures relevant to the
+Additional fields can include external behavioral measures relevant to the
scan. For example vigilance questionnaire score administered after a resting
state scan.
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index d1f98d7062..77bbeb1d82 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -20,7 +20,7 @@ by Ben Inglis:
| HardcopyDeviceSoftwareVersion | (Deprecated) Manufacturer’s designation of the software of the device that created this Hardcopy Image (the printer). Corresponds to DICOM Tag 0018, 101A `Hardcopy Device Software Version` |
| MagneticFieldStrength | RECOMMENDED. Nominal field strength of MR magnet in Tesla. Corresponds to DICOM Tag 0018,0087 `Magnetic Field Strength` |
| ReceiveCoilName | RECOMMENDED. Information describing the receiver coil. Corresponds to DICOM Tag 0018, 1250 `Receive Coil Name`, although not all vendors populate that DICOM Tag, in which case this field can be derived from an appropriate private DICOM field |
-| ReceiveCoilActiveElements | RECOMMENDED. Information describing the active/selected elements of the receiver coil. This doesn’t correspond to a tag in the DICOM ontology. The vendor-defined terminology for active coil elements can go in this field. As an example, for Siemens, coil channels are typically not activated/selected individually, but rather in pre-defined selectable "groups" of individual channels, and the list of the "groups" of elements that are active/selected in any given scan populates the `Coil String` entry in Siemen’s private DICOM fields (e.g., `HEA;HEP` for the Siemens standard 32 ch coil when both the anterior and posterior groups are activated). This is a flexible field that can be used as most appropriate for a given vendor and coil to define the "active" coil elements. Since individual scans can sometimes not have the intended coil elements selected, it is preferable for this field to be populated directly from the DICOM for each individual scan, so that it can be used as a mechanism for checking that a given scan was collected with the intended coil elements selected |
+| ReceiveCoilActiveElements | RECOMMENDED. Information describing the active/selected elements of the receiver coil. This doesn’t correspond to a tag in the DICOM ontology. The vendor-defined terminology for active coil elements can go in this field. As an example, for Siemens, coil channels are typically not activated/selected individually, but rather in pre-defined selectable "groups" of individual channels, and the list of the "groups" of elements that are active/selected in any given scan populates the `Coil String` entry in Siemens’ private DICOM fields (e.g., `HEA;HEP` for the Siemens standard 32 ch coil when both the anterior and posterior groups are activated). This is a flexible field that can be used as most appropriate for a given vendor and coil to define the "active" coil elements. Since individual scans can sometimes not have the intended coil elements selected, it is preferable for this field to be populated directly from the DICOM for each individual scan, so that it can be used as a mechanism for checking that a given scan was collected with the intended coil elements selected |
| GradientSetType | RECOMMENDED. It should be possible to infer the gradient coil from the scanner model. If not, e.g. because of a custom upgrade or use of a gradient insert set, then the specifications of the actual gradient coil should be reported independently |
| MRTransmitCoilSequence | RECOMMENDED. This is a relevant field if a non-standard transmit coil is used. Corresponds to DICOM Tag 0018, 9049 `MR Transmit Coil Sequence` |
| MatrixCoilMode | RECOMMENDED. (If used) A method for reducing the number of independent channels by combining in analog the signals from multiple coil elements. There are typically different default modes when using un-accelerated or accelerated (e.g. GRAPPA, SENSE) imaging |
@@ -119,22 +119,22 @@ sub-/[ses-/]
Anatomical (structural) data acquired for that participant. Currently supported
modalities include:
-| Name | modality_label | Description |
-| :----------------- | :------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T1 weighted | T1w | |
-| T2 weighted | T2w | |
-| T1 Rho map | T1rho | Quantitative T1rho brain imaging` key/value. For example:
```Text
@@ -298,9 +299,9 @@ sequences.
| option E | \[ X ] | | \[ ] | \[ X ] | \[ ] |
**Legend**
-- \[ X ] --> has to be filled
-- \[ \] --> has to be left empty
-- empty cell --> can be specified but not required
+- \[ X ] --> has to be filled
+- \[ \] --> has to be left empty
+- empty cell --> can be specified but not required
##### fMRI task information
@@ -440,8 +441,8 @@ slashes. Here’s an example with multiple target scans:
```JSON
{
- "IntendedFor": ["ses-pre/func/sub-01_task-motor_run-1_bold.nii.gz",
- "ses-post/func/sub-01_task-motor_run-1_bold.nii.gz"]
+ "IntendedFor": ["ses-pre/func/sub-01_ses-pre_task-motor_run-1_bold.nii.gz",
+ "ses-post/func/sub-01_ses-post_task-motor_run-1_bold.nii.gz"]
}
```
diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index fbd6e8a810..d62d3bb863 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -1,8 +1,8 @@
# Magnetoencephalography (MEG)
-Support for MEG was developed as a BIDS Extension Proposal. Please cite the
-following paper when referring to this part of the standard in context of the
-academic literature:
+Support for MEG was developed as a [BIDS Extension Proposal](../06-extensions.md#bids-extension-proposals).
+Please cite the following paper when referring to this part of the standard in
+context of the academic literature:
> Niso Galan, J.G., Gorgolewski, K.J., Bock, E., Brooks, T.L., Flandin, G.,
> Gramfort, A., Henson, R.N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R.,
@@ -18,8 +18,8 @@ Template:
sub-/
[ses-]/
meg/
- sub-[_ses-]_task-[_acq-][_run-][_proc-]_meg.
- [sub-[_ses-]_task-[_acq-][_run-][_proc-]_meg.json]
+ sub-[_ses-]_task-[_run-][_proc-]_meg.
+ [sub-[_ses-]_task-[_run-][_proc-]_meg.json]
```
Unprocessed MEG data MUST be stored in the native file format of the MEG
@@ -54,7 +54,7 @@ trans, quat, mc, etc.), which some installations impose to be run on raw data
because of active shielding software corrections before the MEG data can
actually be exploited.
-### Sidecar JSON document (`*_meg.json`)
+### Sidecar JSON (`*_meg.json`)
Generic fields MUST be present:
@@ -73,10 +73,8 @@ Whenever possible, please avoid using ad-hoc wording.
| Manufacturer | RECOMMENDED. Manufacturer of the MEG system (`CTF`, `Elekta/Neuromag`, `4D/BTi`, `KIT/Yokogawa`, `ITAB`, `KRISS`, `Other`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names |
| ManufacturersModelName | RECOMMENDED. Manufacturer’s designation of the MEG scanner model (e.g. `CTF-275`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names |
| SoftwareVersions | RECOMMENDED. Manufacturer’s designation of the acquisition software. |
-| ManufacturersModelName | RECOMMENDED. Manufacturer’s designation of the MEG scanner model (e.g. `CTF-275`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names |
-| SoftwareVersions | RECOMMENDED. Manufacturer’s designation of the acquisition software. |
| TaskDescription | RECOMMENDED. Description of the task. |
-| Instructions | RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioural or cognitive tasks but also in resting state paradigms (e.g. to distinguish between eyes open and eyes closed). |
+| Instructions | RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (e.g. to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g. Resting State with eyes closed "[http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b)") |
| CogPOID | RECOMMENDED. URL of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (e.g. Rest "[http://wiki.cogpo.org/index.php?title=Rest](http://wiki.cogpo.org/index.php?title=Rest)") |
| DeviceSerialNumber | RECOMMENDED. The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |
@@ -94,42 +92,41 @@ Specific MEG fields MUST be present:
SHOULD be present
-| Field name | Definition |
-| :------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) |
-| MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), `MEGREFChannelCount`=0 |
-| EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) |
-| ECOGChannelCount | RECOMMENDED. Number of ECoG channels |
-| SEEGChannelCount | RECOMMENDED. Number of SEEG channels |
-| EOGChannelCount | RECOMMENDED. Number of EOG channels |
-| ECGChannelCount | RECOMMENDED. Number of ECG channels |
-| EMGChannelCount | RECOMMENDED. Number of EMG channels |
-| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals |
-| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers |
-| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g. 3600) |
-| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) |
-| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g. 1) in case of epoched data |
-| ContinuousHeadLocalization | RECOMMENDED. Boolean (`true` or `false`) value indicating whether continuous head localisation was performed. |
-| HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in 4D/BTi) that track the subject’s head position in the MEG helmet (e.g. `[293, 307, 314, 321]`) |
-| MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) |
-| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g. "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. |
-| AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. `sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds`). |
+| Field name | Definition |
+| :------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) |
+| MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), `MEGREFChannelCount`=0 |
+| EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) |
+| ECOGChannelCount | RECOMMENDED. Number of ECoG channels |
+| SEEGChannelCount | RECOMMENDED. Number of SEEG channels |
+| EOGChannelCount | RECOMMENDED. Number of EOG channels |
+| ECGChannelCount | RECOMMENDED. Number of ECG channels |
+| EMGChannelCount | RECOMMENDED. Number of EMG channels |
+| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals |
+| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers |
+| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g. 3600) |
+| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) |
+| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g. 1) in case of epoched data |
+| ContinuousHeadLocalization | RECOMMENDED. Boolean (`true` or `false`) value indicating whether continuous head localisation was performed. |
+| HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in 4D/BTi) that track the subject’s head position in the MEG helmet (e.g. `[293, 307, 314, 321]`) |
+| MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) |
+| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g. "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. |
+| AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. `sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds`). |
+| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. |
Specific EEG fields (if recorded with MEG) SHOULD be present:
| Field name | Definition |
| :------------------------------ | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| EEGPlacementScheme | OPTIONAL. Placement scheme of EEG electrodes. Either the name of a standardised placement system (e.g., "10-20") or a list of standardised electrode names (e.g. `["Cz", "Pz"]`). |
-| ManufacturersAmplifierModelName | OPTIONAL. Manufacturer’s designation of the EEG amplifier model (e.g., `Biosemi-ActiveTwo`). |
| CapManufacturer | OPTIONAL. Manufacturer of the EEG cap (e.g. `EasyCap`) |
| CapManufacturersModelName | OPTIONAL. Manufacturer’s designation of the EEG cap model (e.g., `M10`) |
| EEGReference | OPTIONAL. Description of the type of EEG reference used (e.g., `M1` for left mastoid, `average`, or `longitudinal bipolar`). |
By construct, EEG when recorded simultaneously with the same MEG system , should
have the same `SamplingFrequency` as MEG. Note that if EEG is recorded with a
-separate amplifier, it should be stored separately under a new /eeg data type
-(see
-[BEP006](https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE/edit#heading=h.4k1noo90gelw)).
+separate amplifier, it should be stored separately under a new `/eeg` data type
+(see [the EEG specification](03-electroencephalography.md)).
Example:
@@ -172,7 +169,7 @@ format `YYYY-MM-DDThh:mm:ss`
example: 2009-06-15T13:45:30. It does not need to be fully detailed, depending
on local REB/IRB ethics board policy.
-## Channels description table (`*_channels.tsv`)
+## Channels description (`*_channels.tsv`)
Template:
@@ -180,7 +177,7 @@ Template:
sub-/
[ses-]/
meg/
- [sub-[_ses-]_task-[_acq-][_run-][_proc-]_channels.tsv]
+ [sub-[_ses-]_task-[_run-][_proc-]_channels.tsv]
```
This file is RECOMMENDED as it provides easily searchable information across
@@ -192,15 +189,15 @@ The columns of the Channels description table stored in `*_channels.tsv` are:
MUST be present:
-| Field name | Definition |
-| :--------- | :----------------------------------------------------------------------------------------------------------------------------------------------------- |
-| name | REQUIRED. Channel name (e.g., MRT012, MEG023) |
-| type | REQUIRED. Type of channel; MUST use the channel types listed below. |
-| units | REQUIRED. Physical unit of the data values recorded by this channel in SI (see [Appendix V](../99-appendices/05-units.md): Units for allowed symbols). |
+| Column name | Definition |
+| :---------- | :----------------------------------------------------------------------------------------------------------------------------------------------------- |
+| name | REQUIRED. Channel name (e.g., MRT012, MEG023) |
+| type | REQUIRED. Type of channel; MUST use the channel types listed below. |
+| units | REQUIRED. Physical unit of the data values recorded by this channel in SI (see [Appendix V](../99-appendices/05-units.md): Units for allowed symbols). |
SHOULD be present:
-| Field name | Definition |
+| Column name | Definition |
| :----------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| description | OPTIONAL. Brief free-text description of the channel, or other information of interest. See examples below. |
| sampling_frequency | OPTIONAL. Sampling rate of the channel in Hz. |
@@ -254,7 +251,7 @@ Restricted keyword list for field `type`
Example of free text for field `description`
-- stimulus, response, vertical EOG, horizontal EOG, skin conductance, sats,
+- stimulus, response, vertical EOG, horizontal EOG, skin conductance, sats,
intracranial, eyetracker
Example:
@@ -267,7 +264,7 @@ UDIO001 TRIG V analog trigger signal
UADC001 AUDIO V envelope of audio signal presented to participant
```
-## Coordinate System JSON document (`*_coordsystem.json`)
+## Coordinate System JSON (`*_coordsystem.json`)
Template:
@@ -347,14 +344,14 @@ Fiducials information:
| FiducialsDescription | OPTIONAL. A freeform text field documenting the anatomical landmarks that were used and how the head localization coils were placed relative to these. This field can describe, for instance, whether the true anatomical locations of the left and right pre-auricular points were used and digitized, or rather whether they were defined as the intersection between the tragus and the helix (the entry of the ear canal), or any other anatomical description of selected points in the vicinity of the ears. |
For more information on the definition of anatomical landmarks, please visit:
-[http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_define](http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
+[http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
For more information on typical coordinate systems for MEG-MRI coregistration:
[http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined),
or:
[http://neuroimage.usc.edu/brainstorm/CoordinateSystems](http://neuroimage.usc.edu/brainstorm/CoordinateSystems)
-### Landmark photos (`*_photo.jpg`)
+## Landmark photos (`*_photo.jpg`)
Photos of the anatomical landmarks and/or head localization coils
(`*_photo.jpg`)
@@ -373,14 +370,18 @@ subject’s head are RECOMMENDED. If the coils are not placed at the location of
actual anatomical landmarks, these latter may be marked with a piece of felt-tip
taped to the skin. Please note that the photos may need to be cropped or blurred
to conceal identifying features prior to sharing, depending on the terms of the
-consent form signed by the participant.
+consent given by the participant.
+
+The `acq` parameter can be used to indicate acquisition of different photos of
+the same face (or other body part in different angles to show, for example, the
+location of the nasion (NAS) as opposed to the right periauricular point (RPA)).
Example of the NAS fiducial placed between the eyebrows, rather than at the
actual anatomical nasion: `sub-0001_ses-001_acq-NAS_photo.jpg`
-### 3-D head point /electrode locations file
+## Head shape and electrode description (`*_headshape.`)
Template:
@@ -393,12 +394,12 @@ sub-/
This file is RECOMMENDED.
-The 3-D locations of head points and/or EEG electrode locations can be digitized
-and stored in separate files. The `*_acq-` can be used when more than one
-type of digitization in done for a session, for example when the head points are
-in a separate file from the EEG locations. These files are stored in the
-specific format of the 3-D digitizer’s manufacturer (see
-[Appendix VI](../99-appendices/06-meg-file-formats.md)).
+The 3-D locations of points that describe the head shape and/or EEG
+electrode locations can be digitized and stored in separate files. The
+`*_acq-` can be used when more than one type of digitization in done for
+a session, for example when the head points are in a separate file from the EEG
+locations. These files are stored in the specific format of the 3-D digitizer’s
+manufacturer (see [Appendix VI](../99-appendices/06-meg-file-formats.md)).
Example:
@@ -413,15 +414,16 @@ Note that the `*_headshape` file(s) is shared by all the runs and tasks in a
session. If the subject needs to be taken out of the scanner and the head-shape
has to be updated, then for MEG it could be considered to be a new session.
-### Empty-room files (`sub-emptyroom`)
+## Empty-room MEG recordings
-Empty-room MEG files capture the environment and system noise. Their collection
-is RECOMMENDED, before/during/after each session. This data is stored inside a
-subject folder named `sub-emptyroom`. The `session label` SHOULD be that of the
-date of the empty-room recording (e.g. `ses-YYYYMMDD`). The `scans.tsv` file
-containing the date/time of the acquisition SHOULD also be included. Hence,
-users will be able to retrieve the empty-room recording that best matches a
-particular session with a participant, based on date/time of recording.
+Empty-room MEG recordings capture the environment and system noise. Their
+collection is RECOMMENDED, before/during/after each session. This data is stored
+inside a subject folder named `sub-emptyroom`. The `session label` SHOULD be
+that of the date of the empty-room recording (e.g. `ses-YYYYMMDD`). The
+`scans.tsv` file containing the date/time of the acquisition SHOULD also be
+included. Hence, users will be able to retrieve the empty-room recording that
+best matches a particular session with a participant, based on date/time of
+recording.
Example:
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
new file mode 100644
index 0000000000..0a5b76a639
--- /dev/null
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -0,0 +1,440 @@
+# Electroencephalography (EEG)
+
+Support for EEG was developed as a [BIDS Extension Proposal](../06-extensions.md#bids-extension-proposals).
+Please cite the following paper when referring to this part of the standard in
+context of the academic literature:
+
+> Pernet, C. R., Appelhoff, S., Flandin, G., Phillips, C., Delorme, A., &
+> Oostenveld, R. (2018, December 6). BIDS-EEG: an extension to the Brain
+> Imaging Data Structure (BIDS) Specification for electroencephalography.
+> [https://doi.org/10.31234/osf.io/63a4y](https://doi.org/10.31234/osf.io/63a4y)
+
+The following example EEG datasets have been formatted using this specification
+and can be used for practical guidance when curating a new dataset.
+
+- Single session per subject: [`eeg_matchingpennies`](https://doi.org/10.17605/OSF.IO/CJ2DR)
+- Multiple sessions per subject: [`eeg_rishikesh`](https://doi.org/10.5281/zenodo.1490922)
+- Combined with fMRI: [`eeg_rest_fmri`](https://osf.io/94c5t/files/)
+
+Further datasets are available from the [BIDS examples repository](https://github.com/bids-standard/bids-examples).
+
+## EEG recording data
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ eeg/
+ sub-[_ses-]_task-[_run-]_eeg.
+ sub-[_ses-]_task-[_run-]_eeg.json
+```
+
+The EEG community uses a variety of formats for storing raw data, and there is
+no single standard that all researchers agree on. For BIDS, EEG data MUST be
+stored in one of the following formats:
+
+- [European data format](https://www.edfplus.info/) (`.edf`)
+
+- [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5)
+ (`.vhdr`, `.vmrk`, `.eeg`) by Brain Products GmbH
+
+- The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab)
+ (`.set` and `.fdt` files)
+
+- [Biosemi](https://www.biosemi.com/) data format (`.bdf`)
+
+It is RECOMMENDED to use the European data format, or the BrainVision data
+format. It is furthermore discouraged to use the other accepted formats over
+these RECOMMENDED formats, particularly because there are conversion scripts
+available in most commonly used programming languages to convert data into the
+RECOMMENDED formats. The data in their original format, if different from the
+supported formats, can be stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
+
+The original data format is especially valuable in case conversion elicits the
+loss of crucial metadata specific to manufacturers and specific EEG systems. We
+also encourage users to provide additional meta information extracted from the
+manufacturer specific data files in the sidecar JSON file. Other relevant files
+MAY be included alongside the original EEG data in `/sourcedata`.
+
+Note that for proper documentation of EEG recording metadata it is important to
+understand the difference between electrode and channel: An EEG electrode is
+attached to the skin, whereas a channel is the combination of the analog
+differential amplifier and analog-to-digital converter that result in a
+potential (voltage) difference that is stored in the EEG dataset. We employ
+the following short definitions:
+
+- Electrode = A single point of contact between the acquisition system and
+ the recording site (e.g., scalp, neural tissue, ...). Multiple electrodes
+ can be organized as caps (for EEG), arrays, grids, leads, strips, probes,
+ shafts, etc.
+
+- Channel = A single analog-to-digital converter in the recording system that
+ regularly samples the value of a transducer, which results in the signal
+ being represented as a time series in the digitized data. This can be
+ connected to two electrodes (to measure the potential difference between
+ them), a magnetic field or magnetic gradient sensor, temperature sensor,
+ accelerometer, etc.
+
+Although the *reference* and *ground* electrodes are often referred to as
+channels, they are in most common EEG systems not recorded by
+themselves. Therefore they are not represented as channels in the data.
+The type of referencing for all channels and optionally the location of
+the reference electrode and the location of the ground electrode MAY
+be specified.
+
+### Sidecar JSON (`*_eeg.json`)
+
+Generic fields MUST be present:
+
+| Field name | Definition |
+| :--------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| TaskName | REQUIRED. Name of the task (for resting state use the `rest` prefix). Different Tasks SHOULD NOT have the same name. The Task label is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. |
+
+SHOULD be present: For consistency between studies and institutions, we
+encourage users to extract the values of these fields from the actual raw data.
+Whenever possible, please avoid using ad hoc wording.
+
+| Field name | Definition |
+| :--------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| InstitutionName | RECOMMENDED. The name of the institution in charge of the equipment that produced the composite instances. |
+| InstitutionAddress | RECOMMENDED. The address of the institution in charge of the equipment that produced the composite instances. |
+| Manufacturer | RECOMMENDED. Manufacturer of the EEG system (e.g., `Biosemi`, `Brain Products`, `Neuroscan`). |
+| ManufacturersModelName | RECOMMENDED. Manufacturer's designation of the EEG system model (e.g., `BrainAmp DC`). |
+| SoftwareVersions | RECOMMENDED. Manufacturer's designation of the acquisition software. |
+| TaskDescription | RECOMMENDED. Description of the task. |
+| Instructions | RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (e.g., to distinguish between eyes open and eyes closed). |
+| CogAtlasID | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g., Resting State with eyes closed "[http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b)"). |
+| CogPOID | RECOMMENDED. URL of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (e.g., Rest "[http://wiki.cogpo.org/index.php?title=Rest](http://wiki.cogpo.org/index.php?title=Rest)") . |
+| DeviceSerialNumber | RECOMMENDED. The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |
+
+Specific EEG fields MUST be present:
+
+| Field name | Definition |
+| :----------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| EEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. |
+| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400). |
+| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60). |
+| SoftwareFilters | REQUIRED. List of temporal software filters applied. Ideally key:value pairs of pre-applied software filters and their parameter values: e.g., `{"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}`. Write `n/a` if no software filters applied. |
+
+SHOULD be present:
+
+| Field name | Definition |
+| :--------------------------| :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| CapManufacturer | RECOMMENDED. Name of the cap manufacturer (e.g., "EasyCap"). |
+| CapManufacturersModelName | RECOMMENDED. Manufacturer's designation of the EEG cap model (e.g., "actiCAP 64 Ch Standard-2"). |
+| EEGChannelCount | RECOMMENDED. Number of EEG channels included in the recording (e.g., 128). |
+| ECGChannelCount | RECOMMENDED. Number of ECG channels. |
+| EMGChannelCount | RECOMMENDED. Number of EMG channels. |
+| EOGChannelCount | RECOMMENDED. Number of EOG channels. |
+| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. |
+| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) trigger. |
+| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). |
+| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`. |
+| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. |
+| HeadCircumference | RECOMMENDED. Circumference of the participants head, expressed in cm (e.g., 58). |
+| EEGPlacementScheme | RECOMMENDED. Placement scheme of EEG electrodes. Either the name of a standardized placement system (e.g., "10-20") or a list of standardized electrode names (e.g., `["Cz", "Pz"]`). |
+| EEGGround | RECOMMENDED. Description of the location of the ground electrode (e.g., "placed on right mastoid (M2)"). |
+| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. |
+| SubjectArtefactDescription | RECOMMENDED. Free-form description of the observed subject artifact and its possible cause (e.g., "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. |
+
+Example:
+
+```JSON
+{
+ "TaskName":"Seeing stuff",
+ "TaskDescription":"Subjects see various images for which phase, amplitude spectrum, and color vary continuously",
+ "Instructions":"Your task is to detect images when they appear for the 2nd time, only then press the response button with your right/left hand (counterbalanced across subjects)",
+ "InstitutionName":"The world best university, 10 Beachfront Avenue, Papeete",
+ "SamplingFrequency":2400,
+ "Manufacturer":"Brain Products",
+ "ManufacturersModelName":"BrainAmp DC",
+ "CapManufacturer":"EasyCap",
+ "CapManufacturersModelName":"M1-ext",
+ "EEGChannelCount":87,
+ "EOGChannelCount":2,
+ "ECGChannelCount":1,
+ "EMGChannelCount":0,
+ "MiscChannelCount":0,
+ "TriggerChannelCount":1,
+ "PowerLineFrequency":50,
+ "EEGPlacementScheme":"10 percent system",
+ "EEGReference":"single electrode placed on FCz",
+ "EEGGround":"placed on AFz",
+ "HardwareFilters":{
+ "ADC's decimation filter (hardware bandwidth limit)":{
+ "-3dB cutoff point (Hz)":480,
+ "Filter order sinc response":5
+ }
+ },
+ "RecordingDuration":600,
+ "RecordingType":"continuous"
+}
+```
+
+Note that the date and time information SHOULD be stored in the Study key file
+([`scans.tsv`](../03-modality-agnostic-files.md#scans-file)). As it is
+indicated there, date time information MUST be expressed in the following
+format `YYYY-MM-DDThh:mm:ss`
+([ISO8601](https://en.wikipedia.org/wiki/ISO_8601) date-time format). For
+example: 2009-06-15T13:45:30. It does not need to be fully detailed, depending
+on local REB/IRB ethics board policy.
+
+## Channels description (`*_channels.tsv`)
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ eeg/
+ [sub-[_ses-]_task-[_run-]_channels.tsv]
+```
+
+Although this information can often be extracted from the EEG recording,
+listing it in a simple `.tsv` document makes it easy to browse or search. The
+required columns are channel `name`, `type` and `units` in this specific order.
+Channel names should furthermore appear in the table in the same order they do
+in the EEG data file. Any number of additional columns may be provided to
+provide additional information about the channels. Note that electrode
+positions should not be added to this file, but to [`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-electrodes-tsv).
+
+The columns of the Channels description table stored in `*_channels.tsv` are:
+
+MUST be present:
+
+| Column name | Definition |
+| :---------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| name | REQUIRED. Channel name (e.g., FC1, Cz) |
+| type | REQUIRED. Type of channel; MUST use the channel types listed below. |
+| units | REQUIRED. Physical unit of the data values recorded by this channel in SI units (see [Appendix V](../99-appendices/05-units.md): Units for allowed symbols). |
+
+SHOULD be present:
+
+| Column name | Definition |
+| :----------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| description | OPTIONAL. Free-form text description of the channel, or other information of interest. See examples below. |
+| sampling_frequency | OPTIONAL. Sampling rate of the channel in Hz. |
+| reference | OPTIONAL. Name of the reference electrode(s) (not needed when it is common to all channels, in that case it can be specified in `*_eeg.json` as `EEGReference`). |
+| low_cutoff | OPTIONAL. Frequencies used for the high-pass filter applied to the channel in Hz. If no high-pass filter applied, use `n/a`. |
+| high_cutoff | OPTIONAL. Frequencies used for the low-pass filter applied to the channel in Hz. If no low-pass filter applied, use `n/a`. Note that hardware anti-aliasing in A/D conversion of all EEG electronics applies a low-pass filter; specify its frequency here if applicable. |
+| notch | OPTIONAL. Frequencies used for the notch filter applied to the channel, in Hz. If no notch filter applied, use `n/a`. |
+| status | OPTIONAL. Data quality observed on the channel `(good/bad)`. A channel is considered `bad` if its data quality is compromised by excessive noise. Description of noise type SHOULD be provided in `[status_description]`. |
+| status_description | OPTIONAL. Free-form text description of noise or artifact affecting data quality on the channel. It is meant to explain why the channel was declared bad in `[status]`. |
+
+Restricted keyword list for field `type` in alphabetic order (shared with the
+MEG and iEEG modality; however, only the types that are common in EEG data are listed here):
+
+| Keyword | Description |
+| :--------| :----------------------------------------------------------- |
+| AUDIO | Audio signal |
+| EEG | Electroencephalogram channel |
+| EOG | Generic electrooculogram (eye), different from HEOG and VEOG |
+| ECG | Electrocardiogram (heart) |
+| EMG | Electromyogram (muscle) |
+| EYEGAZE | Eye tracker gaze |
+| GSR | Galvanic skin response |
+| HEOG | Horizontal EOG (eye) |
+| MISC | Miscellaneous |
+| PUPIL | Eye tracker pupil diameter |
+| REF | Reference channel |
+| RESP | Respiration |
+| SYSCLOCK | System time showing elapsed time since trial started |
+| TEMP | Temperature |
+| TRIG | System triggers |
+| VEOG | Vertical EOG (eye) |
+
+Example of free-form text for field `description`
+
+- n/a, stimulus, response, skin conductance, battery status
+
+Example:
+
+```Text
+name type units description status status_description
+VEOG VEOG microV n/a good n/a
+FDI EMG microV left first dorsal interosseous good n/a
+Cz EEG microV n/a bad high frequency noise
+UADC001 MISC n/a enevelope of audio signal good n/a
+```
+
+## Electrodes description (`*_electrodes.tsv`)
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ eeg/
+ [sub-[_ses-][_acq-][_run-]_electrodes.tsv]
+```
+
+File that gives the location of EEG electrodes. Note that coordinates are
+expected in cartesian coordinates according to the `EEGCoordinateSystem` and
+`EEGCoordinateSystemUnits` fields in `*_coordsystem.json`. **If an
+`*_electrodes.tsv` file is specified, a [`*_coordsystem.json`](#coordinate-system-json-coordsystem-json)
+file MUST be specified as well**. The order of the required columns in the
+`*_electrodes.tsv` file MUST be as listed below.
+
+MUST be present:
+
+| Column name | Definition |
+| :-----------| :------------------------------------------- |
+| name | REQUIRED. Name of the electrode |
+| x | REQUIRED. Recorded position along the x-axis |
+| y | REQUIRED. Recorded position along the y-axis |
+| z | REQUIRED. Recorded position along the z-axis |
+
+SHOULD be present:
+
+| Column name | Definition |
+| :-----------| :-------------------------------------------------------------------------- |
+| type | RECOMMENDED. Type of the electrode (e.g., cup, ring, clip-on, wire, needle) |
+| material | RECOMMENDED. Material of the electrode, e.g., Tin, Ag/AgCl, Gold |
+| impedance | RECOMMENDED. Impedance of the electrode in kOhm |
+
+Example:
+
+```Text
+name x y z type material
+A1 -0.0707 0.0000 -0.0707 clip-on Ag/AgCl
+F3 -0.0567 0.0677 0.0469 cup Ag/AgCl
+Fz 0.0000 0.0714 0.0699 cup Ag/AgCl
+REF -0.0742 -0.0200 -0.0100 cup Ag/AgCl
+GND 0.0742 -0.0200 -0.0100 cup Ag/AgCl
+```
+
+The `acq` parameter can be used to indicate acquisition of the same data. For
+example, this could be the recording of electrode positions with a different
+electrode position recording device, or repeated digitization before and after
+the recording.
+
+## Coordinate System JSON (`*_coordsystem.json`)
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ eeg/
+ [sub-[_ses-][_acq-]_coordsystem.json]
+```
+
+A `*_coordsystem.json` file is used to specify the fiducials, the location of
+anatomical landmarks, and the coordinate system and units in which the position
+of electrodes and landmarks is expressed. **The `*_coordsystem.json` is
+REQUIRED if the optional `*_electrodes.tsv` is specified**. If a corresponding
+anatomical MRI is available, the locations of landmarks and fiducials according
+to that scan should also be stored in the [`*_T1w.json`](./01-magnetic-resonance-imaging-data.md)
+file which goes alongside the MRI data.
+
+For disambiguation, we employ the following definitions for fiducials and
+anatomical landmarks respectively:
+
+- Fiducials = objects with a well defined location used to facilitate the
+ localization of electrodes and co-registration with other geometric data
+ such as the participant's own T1 weighted magnetic resonance head image, a
+ T1 weighted template head image, or a spherical head model. Commonly used
+ fiducials are vitamin-E pills, which show clearly in an MRI, or reflective
+ spheres that are localized with an infrared optical tracking system.
+
+- Anatomical landmarks = locations on a research subject such as the nasion,
+ which is the intersection of the frontal bone and two nasal bones of the
+ human skull.
+
+Fiducials are typically used in conjunction with anatomical landmarks. An
+example would be the placement of vitamin-E pills on top of anatomical
+landmarks, or the placement of LEDs on the nasion and preauricular points to
+triangulate the position of other LED-lit electrodes on a research subject's
+head.
+
+- For more information on the definition of anatomical landmarks, please visit:
+ [http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
+
+- For more information on coordinate systems for coregistration, please visit:
+ [http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
+
+General fields:
+
+| Keyword | Description |
+| :--------------------| :----------------------------------------------------------------------------------------- |
+| IntendedFor | OPTIONAL. Relative path to associate the electrodes, landmarks and fiducials to an MRI/CT. |
+
+Fields relating to the EEG electrode positions:
+
+| Keyword | Description |
+| :------------------------------| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| EEGCoordinateSystem | REQUIRED. Refers to the coordinate system in which the EEG electrode positions are to be interpreted (see [Appendix VIII](../99-appendices/08-coordinate-systems.md)). |
+| EEGCoordinateUnits | REQUIRED. Units in which the coordinates that are listed in the field `EEGCoordinateSystem` are represented (e.g., "mm", "cm"). |
+| EEGCoordinateSystemDescription | RECOMMENDED. Free-form text description of the coordinate system. May also include a link to a documentation page or paper describing the system in greater detail. |
+
+Fields relating to the position of fiducials measured during an EEG session/run:
+
+| Keyword | Description |
+| :---------------------------------------------| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| FiducialsDescription | OPTIONAL. Free-form text description of how the fiducials such as vitamin-E capsules were placed relative to anatomical landmarks, and how the position of the fiducials were measured (e.g., both with Polhemus and with T1w MRI). |
+| FiducialsCoordinates | RECOMMENDED. Key:value pairs of the labels and 3-D digitized position of anatomical landmarks, interpreted following the `FiducialsCoordinateSystem` (e.g., `{"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6], "RPA": [20.2,11.3,9.1]}`). |
+| FiducialsCoordinateSystem | RECOMMENDED. Refers to the coordinate space to which the landmarks positions are to be interpreted - preferably the same as the `EEGCoordinateSystem`. |
+| FiducialsCoordinateUnits | RECOMMENDED. Units in which the coordinates that are listed in the field `AnatomicalLandmarkCoordinateSystem` are represented (e.g., "mm", "cm"). |
+| FiducialsCoordinateSystemDescription | RECOMMENDED. Free-form text description of the coordinate system. May also include a link to a documentation page or paper describing the system in greater detail. |
+
+Fields relating to the position of anatomical landmark measured during an EEG session/run:
+
+| Keyword | Description |
+| :---------------------------------------------| :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| AnatomicalLandmarkCoordinates | RECOMMENDED. Key:value pairs of the labels and 3-D digitized position of anatomical landmarks, interpreted following the `AnatomicalLandmarkCoordinateSystem` (e.g., `{"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6], "RPA": [20.2,11.3,9.1]}`). |
+| AnatomicalLandmarkCoordinateSystem | RECOMMENDED. Refers to the coordinate space to which the landmarks positions are to be interpreted - preferably the same as the `EEGCoordinateSystem`. |
+| AnatomicalLandmarkCoordinateUnits | RECOMMENDED. Units in which the coordinates that are listed in the field `AnatomicalLandmarkCoordinateSystem` are represented (e.g., "mm", "cm"). |
+| AnatomicalLandmarkCoordinateSystemDescription | RECOMMENDED. Free-form text description of the coordinate system. May also include a link to a documentation page or paper describing the system in greater detail. |
+
+If the position of anatomical landmarks is measured using the same system or
+device used to measure electrode positions, and if thereby the anatomical
+landmarks are expressed in the same coordinates, the coordinates of the
+anatomical landmarks can be specified in `electrodes.tsv`. The same applies to
+the coordinates of the fiducials.
+
+Anatomical landmarks or fiducials measured on an anatomical MRI that match the
+landmarks or fiducials during an EEG session/run, must be stored separately in
+the corresponding `*_T1w.json` or `*_T2w.json` file and should be expressed in
+voxels (starting from `[0, 0, 0]`).
+
+Example:
+
+```JSON
+{
+ "IntendedFor":"/sub-01/ses-01/anat/sub-01_T1w.nii",
+ "EEGCoordinateSystem":"Other",
+ "EEGCoordinateUnits":"mm",
+ "EEGCoordinateSystemDescription":"RAS orientation: Origin halfway between LPA and RPA, positive x-axis towards RPA, positive y-axis orthogonal to x-axis through Nasion, z-axis orthogonal to xy-plane, pointing in superior direction.",
+ "FiducialsDescription":"Electrodes and fiducials were digitized with Polhemus, fiducials were recorded as the centre of vitamin E capsules sticked on the left/right pre-auricular and on the nasion, these are also visible on the T1w MRI"
+}
+```
+
+## Landmark photos (`*_photo.jpg`)
+
+Photos of the anatomical landmarks and/or fiducials.
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ eeg/
+ [sub-[_ses-][_acq-]_photo.jpg]
+```
+
+Photos of the anatomical landmarks and/or fiducials are OPTIONAL.
+Please note that the photos may need to be cropped or blurred to conceal
+identifying features prior to sharing, depending on the terms of the consent
+given by the participant.
+
+The `acq` parameter can be used to indicate acquisition of different photos of
+the same face (or other body part in different angles to show, for example, the
+location of the nasion (NAS) as opposed to the right periauricular point (RPA).
+
+Example:
+
+Picture of a NAS fiducial placed between the eyebrows, rather than at the
+actual anatomical nasion: `sub-0001_ses-001_acq-NAS_photo.jpg`
+
+
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
new file mode 100644
index 0000000000..6381299def
--- /dev/null
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -0,0 +1,514 @@
+# intracranial Electroencephalography (iEEG)
+
+Support for iEEG was developed as a [BIDS Extension Proposal](../06-extensions.md#bids-extension-proposals).
+Please cite the following paper when referring to this part of the standard in
+context of the academic literature:
+
+> Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S.,
+> David, O., Devinsky, O., Dichter, B., Flinker, A., Foster, B. L.,
+> Gorgolewski, K. J., Groen, I., Groppe, D., Gunduz, A., Hamilton, L.,
+> Honey, C. J., Jas, M., Knight, R., Lauchaux, J.-P., Lau, J. C.,
+> Lundstrom, B. N., Lee-Messer, C., Miller, K. J., Ojemann, J. G.,
+> Oostenveld, R., Petridou, N., Piantoni, G., Pigorini, A., Pouratian, N.,
+> Ramsey, N. F., Stolk, A., Swann, N. C., Tadel, F., Voytek, B., Wandell, B. A.,
+> Winawer, J., Zehl, L., Hermes, D. (2018, December 13). BIDS-iEEG: an
+> extension to the brain imaging data structure (BIDS) specification for human
+> intracranial electrophysiology. [https://doi.org/10.31234/osf.io/r7vc2](https://doi.org/10.31234/osf.io/r7vc2)
+
+## iEEG recording data
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ ieeg/
+ sub-[_ses-]_task-[_run-]_ieeg.
+ sub-[_ses-]_task-[_run-]_ieeg.json
+```
+
+The iEEG community uses a variety of formats for storing raw data, and there is
+no single standard that all researchers agree on. For BIDS, iEEG data MUST be
+stored in one of the following formats:
+
+- [European Data Format](https://www.edfplus.info/) (`.edf`)
+
+- [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5)
+ (`.vhdr`, `.eeg`, `.vmrk`) by Brain Products GmbH
+
+- The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab)
+ (`.set` and `.fdt` files)
+
+- [Neurodata Without Borders](https://github.com/NeurodataWithoutBorders/pynwb)
+ (`.nwb`)
+
+- [MEF3](http://msel.mayo.edu/codes.html) (`.mef`)
+
+It is RECOMMENDED to use the European data format, or the BrainVision data
+format. It is furthermore discouraged to use the other accepted formats over
+these RECOMMENDED formats, particularly because there are conversion scripts
+available in most commonly used programming languages to convert data into the
+RECOMMENDED formats.
+
+Future versions of BIDS may extend this list of supported file formats. File
+formats for future consideration MUST have open access documentation, MUST have
+open source implementation for both reading and writing in at least two
+programming languages and SHOULD be widely supported in multiple software
+packages. Other formats that may be considered in the future should have a clear
+added advantage over the existing formats and should have wide adoption in the
+BIDS community.
+
+The data format in which the data was originally stored is especially valuable
+in case conversion elicits the loss of crucial metadata specific to
+manufacturers and specific iEEG systems. We also encourage users to provide
+additional meta information extracted from the manufacturer-specific data files
+in the sidecar JSON file. Other relevant files MAY be included alongside the
+original iEEG data in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
+
+### Terminology: Electrodes vs. Channels
+
+For proper documentation of iEEG recording metadata it is important to
+understand the difference between electrode and channel: An iEEG electrode
+is placed on or in the brain, whereas a channel is the combination of the analog
+differential amplifier and analog-to-digital converter that result in a
+potential (voltage) difference that is stored in the iEEG dataset. We employ the
+following short definitions:
+
+- Electrode = A single point of contact between the acquisition system and the
+ recording site (e.g., scalp, neural tissue, ...). Multiple electrodes can be
+ organized as arrays, grids, leads, strips, probes, shafts, caps (for EEG),
+ etc.
+
+- Channel = A single analog-to-digital converter in the recording system that
+ regularly samples the value of a transducer, which results in the signal
+ being represented as a time series in the digitized data. This can be
+ connected to two electrodes (to measure the potential difference between
+ them), a magnetic field or magnetic gradient sensor, temperature sensor,
+ accelerometer, etc.
+
+Although the _reference_ and _ground_ electrodes are often referred to as
+channels, they are in most common iEEG systems not recorded by themselves.
+Therefore they are not represented as channels in the data. The type of
+referencing for all channels and optionally the location of the reference
+electrode and the location of the ground electrode MAY be specified.
+
+### Sidecar JSON (`*_ieeg.json`)
+
+For consistency between studies and institutions, we encourage users to extract
+the values of metadata fields from the actual raw data. Whenever possible,
+please avoid using ad hoc wording.
+
+Generic fields MUST be present:
+
+| Field name | Definition |
+| :----------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| TaskName | REQUIRED. Name of the task (for resting state use the "rest" prefix). No two tasks should have the same name. Task label is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. Note this does not have to be a "behavioral task" that subjects perform, but can reflect some information about the conditions present when the data was acquired (e.g., "rest", "sleep", or "seizure"). |
+
+SHOULD be present: For consistency between studies and institutions, we
+encourage users to extract the values of these fields from the actual raw data.
+Whenever possible, please avoid using ad hoc wording.
+
+| Field name | Definition |
+| :--------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| InstitutionName | RECOMMENDED. The name of the institution in charge of the equipment that produced the composite instances. |
+| InstitutionAddress | RECOMMENDED. The address of the institution in charge of the equipment that produced the composite instances. |
+| Manufacturer | RECOMMENDED. Manufacturer of the amplifier system (e.g., "TDT, Blackrock"). |
+| ManufacturersModelName | RECOMMENDED. Manufacturer's designation of the iEEG amplifier model. |
+| SoftwareVersions | RECOMMENDED. Manufacturer's designation of the acquisition software. |
+| TaskDescription | RECOMMENDED. Longer description of the task. |
+| Instructions | RECOMMENDED. Text of the instructions given to participants before the recording. This is especially important in context of resting state and distinguishing between eyes open and eyes closed paradigms. |
+| CogAtlasID | RECOMMENDED. URL of the corresponding [Cognitive Atlas Task](http://www.cognitiveatlas.org/) term. |
+| CogPOID | RECOMMENDED. URL of the corresponding [CogPO](http://www.cogpo.org/) term. |
+| DeviceSerialNumber | RECOMMENDED. The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |
+
+Specific iEEG fields MUST be present:
+
+| Field name | Definition |
+| :----------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| iEEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "bipolar", "T01" for electrode with name T01, "intracranial electrode on top of a grid, not included with data", "upside down electrode"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. |
+| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the iEEG channels in the recording (e.g., 2400). All other channels should have frequency specified as well in the `channels.tsv` file. |
+| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid where the iEEG recording was done (i.e., 50 or 60). |
+| SoftwareFilters | REQUIRED. List of temporal software filters applied or ideally key:value pairs of pre-applied filters and their parameter values. (n/a if none). E.g., "{'HighPass': {'HalfAmplitudeCutOffHz': 1, 'RollOff: '6dB/Octave'}}". |
+
+Specific iEEG fields SHOULD be present:
+
+| Field name | Definition |
+| :------------------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| DCOffsetCorrection | RECOMMENDED. A description of the method (if any) used to correct for a DC offset. If the method used was subtracting the mean value for each channel, use "mean". |
+| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. |
+| ElectrodeManufacturer | RECOMMENDED. can be used if all electrodes are of the same manufacturer (e.g., AD-TECH, DIXI). If electrodes of different manufacturers are used, please use the corresponding table in the \_electrodes.tsv file. |
+| ElectrodeManufacturersModelName | RECOMMENDED. If different electrode types are used, please use the corresponding table in the \_electrodes.tsv file. |
+| ECOGChannelCount | RECOMMENDED. Number of iEEG surface channels included in the recording (e.g., 120). |
+| SEEGChannelCount | RECOMMENDED. Number of iEEG depth channels included in the recording (e.g., 8). |
+| EEGChannelCount | RECOMMENDED. Number of scalp EEG channels recorded simultaneously (e.g., 21). |
+| EOGChannelCount | RECOMMENDED. Number of EOG channels. |
+| ECGChannelCount | RECOMMENDED. Number of ECG channels. |
+| EMGChannelCount | RECOMMENDED. Number of EMG channels. |
+| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. |
+| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers. |
+| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). |
+| RecordingType | RECOMMENDED. Defines whether the recording is "continuous" or "epoched"; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) |
+| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. If recording was continuous, leave out the field. |
+| iEEGGround | RECOMMENDED. Description of the location of the ground electrode ("placed on right mastoid (M2)"). |
+| iEEGPlacementScheme | RECOMMENDED. Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (e.g., "left frontal grid and bilateral hippocampal depth" or "surface strip and STN depth" or "clinical indication bitemporal, bilateral temporal strips and left grid"). |
+| iEEGElectrodeGroups | RECOMMENDED. Field to describe the way electrodes are grouped into strips, grids or depth probes e.g., {'grid1': "10x8 grid on left temporal pole", 'strip2': "1x8 electrode strip on xxx"}. |
+| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g., "door open", "nurse walked into room at 2 min", "seizure at 10 min"). If this field is left empty, it will be interpreted as absence of artifacts. |
+
+Specific iEEG fields MAY be present:
+
+| Field name | Definition |
+| :------------------------------ | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ElectricalStimulation | OPTIONAL. Boolean field to specify if electrical stimulation was done during the recording (options are "true" or "false"). Parameters for event-like stimulation should be specified in the \_events.tsv file (see example below). |
+| ElectricalStimulationParameters | OPTIONAL. Free form description of stimulation parameters, such as frequency, shape etc. Specific onsets can be specified in the \_events.tsv file. Specific shapes can be described here in freeform text. |
+
+Example:
+
+```JSON
+{
+ "TaskName":"visual",
+ "InstitutionName":"Stanford Hospital and Clinics",
+ "InstitutionAddress":"300 Pasteur Dr, Stanford, CA 94305",
+ "Manufacturer":"Tucker Davis Technologies",
+ "ManufacturersModelName":"n/a",
+ "TaskDescription":"visual gratings and noise patterns",
+ "Instructions":"look at the dot in the center of the screen and press the button when it changes color",
+ "iEEGReference":"left mastoid",
+ "SamplingFrequency":1000,
+ "PowerLineFrequency":60,
+ "SoftwareFilters":"n/a",
+ "DCOffsetCorrection":0,
+ "HardwareFilters":{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dBOctave"}},
+ "ElectrodeManufacturer":"AdTech",
+ "ECOGChannelCount":120,
+ "SEEGChannelCount":0,
+ "EEGChannelCount":0,
+ "EOGChannelCount":0,
+ "ECGChannelCount":0,
+ "EMGChannelCount":0,
+ "MiscChannelCount":0,
+ "TriggerChannelCount":0,
+ "RecordingDuration":233.639,
+ "RecordingType":"continuous",
+ "iEEGGround":"placed on the right mastoid",
+ "iEEGPlacementScheme":"right occipital temporal surface",
+ "ElectricalStimulation":false
+}
+```
+
+Note that the date and time information SHOULD be stored in the Study key file
+([`scans.tsv`](../03-modality-agnostic-files.md#scans-file)). As it is indicated
+there, date time information MUST be expressed in the following format
+`YYYY-MM-DDThh:mm:ss`
+([ISO8601](https://en.wikipedia.org/wiki/ISO_8601) date-time format). For
+example: 2009-06-15T13:45:30. It does not need to be fully detailed, depending
+on local REB/IRB ethics board policy.
+
+## Channels description (`*_channels.tsv`)
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ ieeg/
+ [sub-[_ses-]_task-[_run-]_channels.tsv]
+```
+
+A channel represents one time series recorded with the recording system (for
+example, there can be a bipolar channel, recorded from two electrodes or contact
+points on the tissue). Although this information can often be extracted from the
+iEEG recording, listing it in a simple `.tsv` document makes it easy to browse
+or search (e.g., searching for recordings with a sampling frequency of >=1000
+Hz). The two required columns are channel name and type. Channels should appear
+in the table in the same order they do in the iEEG data file. Any number of
+additional columns may be provided to provide additional information about the
+channels. Note that electrode positions should not be added to this file but to
+`*_electrodes.tsv`.
+
+The columns of the Channels description table stored in \*\_channels.tsv are:
+
+MUST be present:
+
+| Column name | Definition |
+| :----------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| name | REQUIRED. Label of the channel. The label must correspond to \_electrodes.tsv name and all ieeg type channels are required to have a position. The reference channel name MAY be provided in the reference column. |
+| type | REQUIRED. Type of channel, see below for adequate keywords in this field. |
+| units | REQUIRED. Physical unit of the value represented in this channel, e.g., V for Volt, specified according to the [SI unit symbol](https://en.wikipedia.org/wiki/International_System_of_Units#Base_units) and possibly prefix symbol (e.g., mV, μV). For guidelines for Units and Prefixes see [Appendix V](../99-appendices/05-units.md). |
+| low_cutoff | REQUIRED. Frequencies used for the low pass filter applied to the channel in Hz. If no low pass filter was applied, use `n/a`. Note that anti-alias is a low pass filter, specify its frequencies here if applicable. |
+| high_cutoff | REQUIRED. Frequencies used for the high pass filter applied to the channel in Hz. If no high pass filter applied, use `n/a`. |
+
+SHOULD be present:
+
+| Column name | Definition |
+| :----------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| reference | OPTIONAL. Specification of the reference (e.g., 'mastoid', 'ElectrodeName01', 'intracranial', 'CAR', 'other', 'n/a'). If the channel is not an electrode channel (e.g., a microphone channel) use `n/a`. |
+| group | OPTIONAL. Which group of channels (grid/strip/seeg/depth) this channel belongs to. This is relevant because one group has one cable-bundle and noise can be shared. This can be a name or number. Note that any groups specified in `_electrodes.tsv` must match those present here. |
+| sampling_frequency | OPTIONAL. Sampling rate of the channel in Hz. |
+| description | OPTIONAL. Brief free-text description of the channel, or other information of interest (e.g., position (e.g., "left lateral temporal surface", etc.). |
+| notch | OPTIONAL. Frequencies used for the notch filter applied to the channel, in Hz. If no notch filter applied, use n/a. |
+| status | OPTIONAL. Data quality observed on the channel (good/bad). A channel is considered bad if its data quality is compromised by excessive noise. Description of noise type SHOULD be provided in `[status_description]`. |
+| status_description | OPTIONAL. Freeform text description of noise or artifact affecting data quality on the channel. It is meant to explain why the channel was declared bad in `[status]`. |
+
+**Example** `sub-01_channels.tsv`:
+
+```Text
+name type units low_cutoff high_cutoff status status_description
+LT01 ECOG μV 300 0.11 good n/a
+LT02 ECOG μV 300 0.11 bad broken
+H01 SEEG μV 300 0.11 bad line_noise
+ECG1 ECG μV n/a 0.11 good n/a
+TR1 TRIG n/a n/a n/a good n/a
+```
+Restricted keyword list for field type in alphabetic order (shared with the MEG
+and EEG modality; however, only types that are common in iEEG data are listed here):
+
+| Keyword | Description |
+| :------- | :--------------------------------------------------------------------- |
+| EEG | Electrode channel from electroencephalogram |
+| ECOG | Electrode channel from electrocorticogram (intracranial) |
+| SEEG | Electrode channel from stereo-electroencephalogram (intracranial) |
+| DBS | Electrode channel from deep brain stimulation electrode (intracranial) |
+| VEOG | Vertical EOG (electrooculogram) |
+| HEOG | Horizontal EOG |
+| EOG | Generic EOG channel if HEOG or VEOG information not available |
+| ECG | ElectroCardioGram (heart) |
+| EMG | ElectroMyoGram (muscle) |
+| TRIG | System Triggers |
+| AUDIO | Audio signal |
+| PD | Photodiode |
+| EYEGAZE | Eye Tracker gaze |
+| PUPIL | Eye Tracker pupil diameter |
+| MISC | Miscellaneous |
+| SYSCLOCK | System time showing elapsed time since trial started |
+| ADC | Analog to Digital input |
+| DAC | Digital to Analog output |
+| REF | Reference channel |
+| OTHER | Any other type of channel |
+
+The free text field for the channel description can for example be specified as
+intracranial, stimulus, response, vertical EOG, horizontal EOG, skin
+conductance, eyetracker, etc.
+
+## Electrode description (`*_electrodes.tsv`)
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ ieeg/
+ sub-[_ses-][_space-]_electrodes.tsv
+```
+
+File that gives the location, size and other properties of iEEG electrodes. Note
+that coordinates are expected in cartesian coordinates according to the
+`iEEGCoordinateSystem` and `iEEGCoordinateSystemUnits` fields in
+`*_coordsystem.json`. If an `*_electrodes.tsv` file is specified, a
+`*_coordsystem.json` file MUST be specified as well.
+
+The optional space label (`*[_space-]_electrodes.tsv`) can be used to
+indicate the way in which electrode positions are interpreted. The space label
+needs to be taken from the list in
+[Appendix VIII](../99-appendices/08-coordinate-systems.md)
+
+For examples:
+
+- `_space-MNI152Lin` (electrodes are coregistred and scaled to a specific MNI
+ template)
+
+- `_space-Talairach` (electrodes are coregistred and scaled to Talairach
+ space)
+
+When referring to the `*_electrodes.tsv` file in a certain _space_ as defined
+above, the `space-` of the accompanying `*_coordsystem.json` MUST
+correspond.
+
+For example:
+
+- `sub-01_space-Talairach_electrodes.tsv`
+- `sub-01_space-Talairach_coordsystem.json`
+
+The order of the required columns in the `*_electrodes.tsv` file MUST be as
+listed below.
+
+MUST be present:
+
+| Column name | Definition |
+| :----------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| name | REQUIRED. Name of the electrode contact point. |
+| x | REQUIRED. X position. The positions of the center of each electrode in xyz space. Units are in millimeters or pixels and are specified in \_\*space-\_electrode.json. |
+| y | REQUIRED. Y position. |
+| z | REQUIRED. Z position. If electrodes are in 2D space this should be a column of n/a values. |
+| size | REQUIRED. Surface area of the electrode, in mm^2. |
+
+SHOULD be present:
+
+| Column name | Definition |
+| :----------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| material | OPTIONAL. Material of the electrodes. |
+| manufacturer | OPTIONAL. Recommended field to specify the manufacturer for each electrode. Can be used if electrodes were manufactured by more than one company. |
+| group | OPTIONAL. Optional field to specify the group that the electrode is a part of. Note that any group specified here should match a group specified in `_channels.tsv`. |
+| hemisphere | OPTIONAL. Optional field to specify the hemisphere in which the electrode is placed, one of `['L' or 'R']` (use capital). |
+
+MAY be present:
+
+| Column name | Definition |
+| :---------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| type | OPTIONAL. Optional type of the electrode, e.g., cup, ring, clip-on, wire, needle, ... |
+| impedance | OPTIONAL. Impedance of the electrode in kOhm. |
+| dimension | OPTIONAL. Size of the group (grid/strip/probe) that this electrode belongs to. Must be of form `[AxB]` with the smallest dimension first (e.g., `[1x8]`). |
+
+Example:
+
+```Text
+name x y z size manufacturer
+LT01 19 -39 -16 2.3 Integra
+LT02 23 -40 -19 2.3 Integra
+H01 27 -42 -21 5 AdTech
+```
+
+## Coordinate System JSON (`*_coordsystem.json`)
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ ieeg/
+ sub-[_ses-][_space-]_coordsystem.json
+```
+
+This `_coordsystem.json` file contains the coordinate system in which electrode
+positions are expressed. The associated MRI, CT, X-Ray, or operative photo can
+also be specified.
+
+General fields:
+
+| Field name | Definition |
+| :---------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| IntendedFor | RECOMMENDED. This can be an MRI/CT or a file containing the operative photo, x-ray or drawing with path relative to the project folder. If only a surface reconstruction is available, this should point to the surface reconstruction file. Note that this file should have the same coordinate system specified in `iEEGCoordinateSystem`. For example, **T1**: `sub-/ses-/anat/sub-01_T1w.nii.gz` **Surface**: `/derivatives/surfaces/sub-/ses-/anat/sub-01_T1w_pial.R.surf.gii` **Operative photo**: `/sub-/ses-/ieeg/sub-0001_ses-01_acq-photo1_photo.jpg` **Talairach**: `/derivatives/surfaces/sub-Talairach/ses-01/anat/sub-Talairach_T1w_pial.R.surf.gii` |
+
+Fields relating to the iEEG electrode positions:
+
+| Field name | Definition |
+| :---------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| iEEGCoordinateSystem | REQUIRED. Defines the coordinate system for the iEEG electrodes. See [Appendix VIII](../99-appendices/08-coordinate-systems.md) for a list of restricted keywords. If positions correspond to pixel indices in a 2D image (of either a volume-rendering, surface-rendering, operative photo, or operative drawing), this must be "Pixels". For more information, see the section on [2D coordinate systems](../04-modality-specific-files/04-intracranial-electroencephalography.md#Allowed-2D-coordinate-systems). |
+| iEEGCoordinateUnits | REQUIRED. Units of the \_electrodes.tsv, MUST be "m", "mm", "cm" or "pixels". |
+| iEEGCoordinateSystemDescription | RECOMMENDED. Freeform text description or link to document describing the iEEG coordinate system system in detail (e.g., "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right"). |
+| iEEGCoordinateProcessingDescription | RECOMMENDED. Has any post-processing (such as projection) been done on the electrode positions (e.g., "surface_projection", "none"). |
+| iEEGCoordinateProcessingReference | RECOMMENDED. A reference to a paper that defines in more detail the method used to localize the electrodes and to post-process the electrode positions. . |
+
+### Recommended 3D coordinate systems
+
+It is preferred that electrodes are localized in a 3D coordinate system (with
+respect to a pre- and/or post-operative anatomical MRI or CT scans or in a
+standard space as specified in BIDS [Appendix VIII](../99-appendices/08-coordinate-systems.md)
+about preferred names of coordinate systems, such as ACPC).
+
+### Allowed 2D coordinate systems
+
+If electrodes are localized in 2D space (only x and y are specified and z is
+n/a), then the positions in this file must correspond to the locations expressed
+in pixels on the photo/drawing/rendering of the electrodes on the brain. In this
+case, coordinates must be (row,column) pairs, with (0,0) corresponding to the
+upper left pixel and (N,0) corresponding to the lower left pixel.
+
+### Multiple coordinate systems
+
+If electrode positions are known in multiple coordinate systems (e.g., MRI, CT
+and MNI), these spaces can be distinguished by the optional `[_space-]`
+field, see the [`*_electrodes.tsv`-section](../04-modality-specific-files/04-intracranial-electroencephalography.md#electrode-description-space-label-electrodes-tsv)
+for more information. Note that the `[_space-]` fields must correspond
+between `*_electrodes.tsv` and `*_coordsystem.json` if they refer to the same
+data.
+
+Example:
+
+```json
+{
+ "IntendedFor": "/sub-01/ses-01/anat/sub-01_T1w.nii.gz",
+ "iEEGCoordinateSystem": "ACPC",
+ "iEEGCoordinateUnits": "mm",
+ "iEEGCoordinateSystemDescription": "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right",
+ "iEEGCoordinateProcessingDescription": "surface_projection",
+ "iEEGCoordinateProcessingReference": "Hermes et al., 2010 JNeuroMeth"
+}
+```
+
+## Photos of the electrode positions (`*_photo.jpg`)
+
+Template:
+
+```Text
+sub-/
+ [ses-]/
+ ieeg/
+ sub-[_ses-][_acq-`, with labels chosen by the researcher and
+optionally defined in more detail in an accompanying `_events.json` file (as
+per the main BIDS spec). Functions for complex stimulation patterns can, similar
+as when a video is presented, be stored in a folder in the `/stimuli/` folder.
+For example: `/stimuli/electrical_stimulation_functions/biphasic.tsv`
+
+Example:
+
+```Text
+onset duration trial_type electrical_stimulation_type electrical_stimulation_site electrical_stimulation_current
+1.2 0.001 electrical_stimulation biphasic LT01-LT02 0.005
+1.3 0.001 electrical_stimulation biphasic LT01-LT02 0.005
+2.2 0.001 electrical_stimulation biphasic LT02-LT03 0.005
+4.2 1 electrical_stimulation complex LT02-LT03 n/a
+15.2 3 auditory_stimulus n/a n/a n/a
+```
diff --git a/src/04-modality-specific-files/03-task-events.md b/src/04-modality-specific-files/05-task-events.md
similarity index 87%
rename from src/04-modality-specific-files/03-task-events.md
rename to src/04-modality-specific-files/05-task-events.md
index 966762e304..35a9e751ec 100644
--- a/src/04-modality-specific-files/03-task-events.md
+++ b/src/04-modality-specific-files/05-task-events.md
@@ -31,9 +31,11 @@ REQUIRED and OPTIONAL columns:
| :------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| onset | REQUIRED. Onset (in seconds) of the event measured from the beginning of the acquisition of the first volume in the corresponding task imaging data file. If any acquired scans have been discarded before forming the imaging data file, ensure that a time of 0 corresponds to the first image stored. In other words negative numbers in "onset" are allowed5 . |
| duration | REQUIRED. Duration of the event (measured from onset) in seconds. Must always be either zero or positive. A "duration" value of zero implies that the delta function or event is so short as to be effectively modeled as an impulse. |
+| sample | OPTIONAL. Onset of the event according to the sampling scheme of the recorded modality (i.e., referring to the raw data file that the `events.tsv` file accompanies). |
| trial_type | OPTIONAL. Primary categorisation of each trial to identify them as instances of the experimental conditions. For example: for a response inhibition task, it could take on values "go" and "no-go" to refer to response initiation and response inhibition experimental conditions. |
| response_time | OPTIONAL. Response time measured in seconds. A negative response time can be used to represent preemptive responses and "n/a" denotes a missed response. |
| stim_file | OPTIONAL. Represents the location of the stimulus file (image, video, sound etc.) presented at the given onset time. There are no restrictions on the file formats of the stimuli files, but they should be stored in the /stimuli folder (under the root folder of the dataset; with optional subfolders). The values under the stim_file column correspond to a path relative to "/stimuli". For example "images/cat03.jpg" will be translated to "/stimuli/images/cat03.jpg". |
+| value | OPTIONAL. Marker value associated with the event (e.g., the value of a TTL trigger that was recorded at the onset of the event). |
| HED | OPTIONAL. Hierarchical Event Descriptor (HED) Tag. See [Appendix III](../99-appendices/03-hed.md) for details. |
5 For example in case there is an in scanner training phase that
diff --git a/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
similarity index 61%
rename from src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md
rename to src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
index b4236af057..2e2e0fe5ce 100644
--- a/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md
+++ b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
@@ -22,17 +22,24 @@ directory. For example:`task-movie_stim.tsv.gz`
Physiological recordings such as cardiac and respiratory signals and other
continuous measures (such as parameters of a film or audio stimuli) can be
specified using two files: a gzip compressed TSV file with data (without header
-line) and a JSON for storing start time, sampling frequency, and name of the
-columns from the TSV. Please note that in contrast to other TSV files this one
-does not include a header line. Instead the name of columns are specified in the
-JSON file. This is to improve compatibility with existing software (FSL PNM) as
-well as make support for other file formats possible in the future. Start time
-should be expressed in seconds in relation to the time of start of acquisition
-of the first volume in the corresponding imaging file (negative values are
-allowed). Sampling frequency should be expressed in Hz. Recordings with
-different sampling frequencies and/or starting times should be stored in
-separate files. The following naming conventions should be used for column
-names:
+line) and a JSON for storing the following metadata fields:
+
+| Field name | Definition |
+| :---------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| SamplingFrequency | REQUIRED. Sampling frequency in Hz of all columns in the file. |
+| StartTime | REQUIRED. Start time in seconds in relation to the start of acquisition of the first data sample in the corresponding neural dataset (negative values are allowed). |
+| Columns | REQUIRED. Names of columns in file. |
+
+Additional metadata may be included as in
+[any TSV file](../02-common-principles.md#tabular-files) to specify, for
+example, the units of the recorded time series.
+Please note that in contrast to other TSV files this one does not include a
+header line. Instead the name of columns are specified in the JSON file.
+This is to improve compatibility with existing software (FSL PNM) as
+well as make support for other file formats possible in the future.
+Recordings with different sampling frequencies and/or starting times should be
+stored in separate files.
+The following naming conventions should be used for column names:
| Column name | Definition |
| :---------- | :--------------------------------------------------- |
@@ -90,6 +97,9 @@ sub-control01/
{
"SamplingFrequency": 100.0,
"StartTime": -22.345,
- "Columns": ["cardiac", "respiratory", "trigger"]
+ "Columns": ["cardiac", "respiratory", "trigger"],
+ "cardiac": {
+ "Units": "mV"
+ }
}
```
diff --git a/src/04-modality-specific-files/05-behavioural-experiments.md b/src/04-modality-specific-files/07-behavioral-experiments.md
similarity index 100%
rename from src/04-modality-specific-files/05-behavioural-experiments.md
rename to src/04-modality-specific-files/07-behavioral-experiments.md
diff --git a/src/04-modality-specific-files/images/ieeg_electrodes1.png b/src/04-modality-specific-files/images/ieeg_electrodes1.png
new file mode 100644
index 0000000000..244bdd66c4
Binary files /dev/null and b/src/04-modality-specific-files/images/ieeg_electrodes1.png differ
diff --git a/src/04-modality-specific-files/images/ieeg_electrodes2.png b/src/04-modality-specific-files/images/ieeg_electrodes2.png
new file mode 100644
index 0000000000..7dfd425a31
Binary files /dev/null and b/src/04-modality-specific-files/images/ieeg_electrodes2.png differ
diff --git a/src/06-extensions.md b/src/06-extensions.md
index 6769a7cdcd..a6d081060a 100644
--- a/src/06-extensions.md
+++ b/src/06-extensions.md
@@ -7,17 +7,15 @@ This page lists some ways that you can get involved with the BIDS community.
There are many ways to get involved with the BIDS community!
### The BIDS Starter Kit
-If you're new
-to the BIDS community and you'd like to learn a bit more, we recommend checking
-out the [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit/blob/master/README.md).
+If you're new to the BIDS community and you'd like to learn a bit more, we
+recommend checking out the [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit/blob/master/README.md).
This has introductory information about the BIDS specification, tools in the
BIDS ecosystem, and how you can get involved.
### The BIDS Contributor guide
If you'd like to get involved more heavily in helping extend the BIDS
-specification or develop tools for it, see the
-[BIDS Contributor Guide](https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/edit?usp%3Dsharing&sa=D&ust=1537468908724000).
+specification or develop tools for it, see the [BIDS Contributor Guide](https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4).
It contains more in-depth information for getting involved with the BIDS
community.
@@ -27,36 +25,44 @@ The BIDS specification can be extended in a backwards compatible way and will
evolve over time. These are accomplished with BIDS Extension Proposals (BEPs),
which are community-driven processes.
-Below is a table of currently-active BEPs.
-
-| Extension label | Title | Moderators/leads |
-| :---------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------- |
-| [BEP001](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg) | [Structural acquisitions that include multiple contrasts (multi echo, flip angle, inversion time) sequences](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg) | Gilles de Hollander |
-| [BEP002](https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M) | [The BIDS Models Specification](https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M) | Tal Yarkoni |
-| [BEP003](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4) | [Common Derivatives](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4) | Chris Gorgolewski |
-| [BEP004](https://docs.google.com/document/d/1kyw9mGgacNqeMbp4xZet3RnDhcMmf4_BmRgKaOkO2Sc) | [Susceptibility Weighted Imaging (SWI)](https://docs.google.com/document/d/1kyw9mGgacNqeMbp4xZet3RnDhcMmf4_BmRgKaOkO2Sc) | Fidel Alfaro Almagro |
-| [BEP005](https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c) | [Arterial Spin Labeling (ASL)](https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c) | Henk-Jan Mutsaerts and Michael Chappell |
-| [BEP006](https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE) | [Electroencephalography (EEG)](https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE) | Cyril R Pernet, Robert Oostenveld, Stefan Appelhoff |
-| [BEP009](https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0) | [Positron Emission Tomography (PET)](https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0) | Melanie Ganz |
-| [BEP010](https://docs.google.com/document/d/1qMUkoaXzRMlJuOcfTYNr3fTsrl4SewWjffjMD5Ew6GY) | [intracranial Electroencephalography (iEEG)](https://docs.google.com/document/d/1qMUkoaXzRMlJuOcfTYNr3fTsrl4SewWjffjMD5Ew6GY) | Dora Hermes and Chris Holdgraf |
-| [BEP011](https://docs.google.com/document/d/1YG2g4UkEio4t_STIBOqYOwneLEs1emHIXbGKynx7V0Y) | [The structural preprocessing derivatives](https://docs.google.com/document/d/1YG2g4UkEio4t_STIBOqYOwneLEs1emHIXbGKynx7V0Y) | Andrew Hoopes |
-| [BEP012](https://docs.google.com/document/d/16CvBwVMAs0IMhdoKmlmcm3W8254dQmNARo-7HhE-lJU) | [The functional preprocessing derivatives](https://docs.google.com/document/d/16CvBwVMAs0IMhdoKmlmcm3W8254dQmNARo-7HhE-lJU) | Camille Maumet and Chris Markiewicz |
-| [BEP013](https://docs.google.com/document/d/1qBNQimDx6CuvHjbDvuFyBIrf2WRFUOJ-u50canWjjaw) | [The resting state fMRI derivatives](https://docs.google.com/document/d/1qBNQimDx6CuvHjbDvuFyBIrf2WRFUOJ-u50canWjjaw) | Steven Giavasis |
-| [BEP014](https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE) | [The affine transformations and nonlinear field warps](https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE) | Oscar Esteban |
-| [BEP015](https://docs.google.com/document/d/1WYOTXDB7GzlHoWqLjd45I3uGBgPxXddST-NTqBnroJE) | [Mapping file](https://docs.google.com/document/d/1WYOTXDB7GzlHoWqLjd45I3uGBgPxXddST-NTqBnroJE) | Eric Earl, Camille Maumet, and Vasudev Raguram |
-| [BEP016](https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60) | [The diffusion weighted imaging derivatives](https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60) | Franco Pestilli and Oscar Esteban |
-| [BEP017](https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA) | [Generic BIDS connectivity data schema](https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA) | Eugene Duff and Paul McCarthy |
-| [BEP018](https://docs.google.com/document/d/1uRkgyzESLKuGjXi98Z97Wh6vt-iLN5nOAb9TG16CjUs) | [Genetic information](https://docs.google.com/document/d/1uRkgyzESLKuGjXi98Z97Wh6vt-iLN5nOAb9TG16CjUs) | Cyril R Pernet, Clara Moreau, and Thomas Nichols |
-| [BEP019](https://docs.google.com/document/d/1FqJI791ycXr0bfRg2qyLqAf0RpVttJ2cInOgMWrKsNU) | [DICOM Metadata](https://docs.google.com/document/d/1FqJI791ycXr0bfRg2qyLqAf0RpVttJ2cInOgMWrKsNU) | Satrajit Ghosh |
-| [BEP020](https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw) | [Eye Tracking including Gaze Position and Pupil Size(ET)](https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw) | Benjamin Gagl and Dejan Draschkow |
-| [BEP021](https://docs.google.com/document/d/1PmcVs7vg7Th-cGC-UrX8rAhKUHIzOI-uIOh69_mvdlw) | [Common Electrophysiological Derivatives](https://docs.google.com/document/d/1PmcVs7vg7Th-cGC-UrX8rAhKUHIzOI-uIOh69_mvdlw) | Stefan Appelhoff, Cyril Pernet, Robert Oostenveld, Teon Brooks |
-| [BEP022](https://docs.google.com/document/d/1pWCb02YNv5W-UZZja24fZrdXLm4X7knXMiZI7E2z7mY) | [Magnetic Resonance Spectroscopy (MRS)](https://docs.google.com/document/d/1pWCb02YNv5W-UZZja24fZrdXLm4X7knXMiZI7E2z7mY) | Dickson Wong |
-| [BEP023](https://docs.google.com/document/d/1yzsd1J9GT-aA0DWhdlgNr5LCu6_gvbjLyfvYq2FuxlY) | [PET Preprocessing derivatives](https://docs.google.com/document/d/1yzsd1J9GT-aA0DWhdlgNr5LCu6_gvbjLyfvYq2FuxlY) | Martin Noergaard, Graham Searle, Melanie Ganz |
-| [BEP024](https://docs.google.com/document/d/1fqnJZ18x5LJC8jiJ8yvPHUGFzNBZ6gW2kywYrUKWtuo) | [Computed Tomography scan (CT)](https://docs.google.com/document/d/1fqnJZ18x5LJC8jiJ8yvPHUGFzNBZ6gW2kywYrUKWtuo) | Hugo Boniface |
+Below is a table of currently-active BEPs. The "Extension label" column
+provides a direct link to the documentation.
+
+| Extension label | Title | Moderators/leads |
+| :---------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------- |
+| [BEP001](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg) | Structural acquisitions that include multiple contrasts (multi echo, flip angle, inversion time) sequences | Gilles de Hollander |
+| [BEP002](https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M) | The BIDS Models Specification | Tal Yarkoni |
+| [BEP003](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4) | Common Derivatives | Chris Gorgolewski |
+| [BEP004](https://docs.google.com/document/d/1kyw9mGgacNqeMbp4xZet3RnDhcMmf4_BmRgKaOkO2Sc) | Susceptibility Weighted Imaging (SWI) | Fidel Alfaro Almagro |
+| [BEP005](https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c) | Arterial Spin Labeling (ASL) | Henk-Jan Mutsaerts and Michael Chappell |
+| [BEP009](https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0) | Positron Emission Tomography (PET) | Melanie Ganz |
+| [BEP011](https://docs.google.com/document/d/1YG2g4UkEio4t_STIBOqYOwneLEs1emHIXbGKynx7V0Y) | The structural preprocessing derivatives | Andrew Hoopes |
+| [BEP012](https://docs.google.com/document/d/16CvBwVMAs0IMhdoKmlmcm3W8254dQmNARo-7HhE-lJU) | The functional preprocessing derivatives | Camille Maumet and Chris Markiewicz |
+| [BEP013](https://docs.google.com/document/d/1qBNQimDx6CuvHjbDvuFyBIrf2WRFUOJ-u50canWjjaw) | The resting state fMRI derivatives | Steven Giavasis |
+| [BEP014](https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE) | The affine transformations and nonlinear field warps | Oscar Esteban |
+| [BEP015](https://docs.google.com/document/d/1WYOTXDB7GzlHoWqLjd45I3uGBgPxXddST-NTqBnroJE) | Mapping file | Eric Earl, Camille Maumet, and Vasudev Raguram |
+| [BEP016](https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60) | The diffusion weighted imaging derivatives | Franco Pestilli and Oscar Esteban |
+| [BEP017](https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA) | Generic BIDS connectivity data schema | Eugene Duff and Paul McCarthy |
+| [BEP018](https://docs.google.com/document/d/1uRkgyzESLKuGjXi98Z97Wh6vt-iLN5nOAb9TG16CjUs) | Genetic information | Cyril R Pernet, Clara Moreau, and Thomas Nichols |
+| [BEP019](https://docs.google.com/document/d/1FqJI791ycXr0bfRg2qyLqAf0RpVttJ2cInOgMWrKsNU) | DICOM Metadata | Satrajit Ghosh |
+| [BEP020](https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw) | Eye Tracking including Gaze Position and Pupil Size(ET) | Benjamin Gagl and Dejan Draschkow |
+| [BEP021](https://docs.google.com/document/d/1PmcVs7vg7Th-cGC-UrX8rAhKUHIzOI-uIOh69_mvdlw) | Common Electrophysiological Derivatives | Mainak Jas, Stefan Appelhoff, Cyril Pernet, Robert Oostenveld, Teon Brooks |
+| [BEP022](https://docs.google.com/document/d/1pWCb02YNv5W-UZZja24fZrdXLm4X7knXMiZI7E2z7mY) | Magnetic Resonance Spectroscopy (MRS) | Dickson Wong |
+| [BEP023](https://docs.google.com/document/d/1yzsd1J9GT-aA0DWhdlgNr5LCu6_gvbjLyfvYq2FuxlY) | PET Preprocessing derivatives | Martin Noergaard, Graham Searle, Melanie Ganz |
+| [BEP024](https://docs.google.com/document/d/1fqnJZ18x5LJC8jiJ8yvPHUGFzNBZ6gW2kywYrUKWtuo) | Computed Tomography scan (CT) | Hugo Boniface |
+| [BEP025](https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4) | Medical Population Imaging Data structure (MIDS) | Jose Manuel Saborit Torres |
+| [BEP026](https://docs.google.com/document/d/14KC1d5-Lx-7ZSMtwS7pVAAvz-2WR_uoo5FvsNirzqJw) | Microelectrode Recordings (MER) | Greydon Gilmore |
When an extension reaches maturity it is merged into the main body of the
-specification.
+specification. Below is a table of BEPs that have been merged in the main body
+of the specification.
+
+| Extension label | Title | Moderators/leads |
+| :---------------------------------------------------------------------------------------- | :----------------------------------------- | :------------------------------------------------ |
+| [BEP006](https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE) | Electroencephalograpgy (EEG) | Cyril Pernet, Stefan Appelhoff, Robert Oostenveld |
+| [BEP008](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM) | Magnetoencephalography (MEG) | Guiomar Niso |
+| [BEP010](https://docs.google.com/document/d/1qMUkoaXzRMlJuOcfTYNr3fTsrl4SewWjffjMD5Ew6GY) | intracranial Electroencephalograpgy (iEEG) | Chris Holdgraf, Dora Hermes |
All of the extension ideas that are not backwards compatible and thus
will have to wait for BIDS 2.0 are listed
-[here](https://docs.google.com/document/d/1LEgsMiisGDe1Gv-hBp1EcLmoz7AlKj6VYULUgDD3Zdw)
+[here](https://docs.google.com/document/d/1LEgsMiisGDe1Gv-hBp1EcLmoz7AlKj6VYULUgDD3Zdw).
diff --git a/src/99-appendices/01-contributors.md b/src/99-appendices/01-contributors.md
index 7655e4da08..807cf90751 100644
--- a/src/99-appendices/01-contributors.md
+++ b/src/99-appendices/01-contributors.md
@@ -30,81 +30,87 @@ The following individuals have contributed to the Brain Imaging Data Structure
ecosystem (in alphabetical order). If you contributed to the BIDS ecosystem and
your name is not listed, please add it.
-- Stefan Appelhoff 📖💬🤔🐛💡💻
-- Tibor Auer 💬📖💡🔧📢
-- Sylvain Baillet 📖🔍
-- Elizabeth Bock 📖💡
-- Eric Bridgeford 📖🔧
-- Teon L. Brooks 📖💻⚠️💬👀🤔🔧🐛📢
-- Suyash Bhogawar 📖💡⚠️🔧💬
-- Vince D. Calhoun 📖
-- Alexander L. Cohen 🐛💻📖💬
-- R. Cameron Craddock 📖📢
-- Samir Das 📖
-- Alejandro de la Vega 🐛💻⚠️
-- Eugene P. Duff 📖
-- Elizabeth DuPre 📖💡🔍🤔
-- Eric A. Earl 🤔
-- Anders Eklund 📖📢💻
-- Franklin W. Feingold 📋📝✅
-- Guillaume Flandin 📖💻
-- Remi Gau 📖💻
-- Satrajit S. Ghosh 📖💻
-- Tristan Glatard 📖💻
-- Mathias Goncalves 💻🔧📢
-- Krzysztof J. Gorgolewski 📖💻💬🤔🔍📢📝💡🔌
-- Alexandre Gramfort 📖💡
-- Jeffrey S. Grethe 💬🐛✅📢
-- Yaroslav O. Halchenko 📖📢🔧💬🐛
-- Daniel A. Handwerker 📖
-- Michael Hanke 📖🤔🔧🐛📢
-- Michael P. Harms 📖⚠️🔧
-- Richard N. Henson 📖
-- Dora Hermes 📖💻✅🔍🤔
-- Katja Heuer 🔧
-- Chris Holdgraf 📖🤔
-- Jean-Christophe Houde 📖
-- International Neuroinformatics Coordinating Facility 💵📋
-- Mainak Jas 📖💻
-- David Keator 📖
-- James Kent 💬💻
-- Gregory Kiar 📖💻🎨🔧
-- Pamela LaMontagne 📖💡
-- Kevin Larcher 💬
-- Laura and John Arnold Foundation 💵
-- Xiangrui Li 📖💻
-- Vladimir Litvak 📖
-- Dan Lurie 🤔📖🔧🔌💻💬
-- Camille Maumet 📖
-- Christopher J. Markiewicz 💬📖💻
-- Jeremy Moreau 📖💡
-- Zachary Michael 📖
-- Michael P. Milham 💡🔍
-- Henk Mutsaerts 📖
-- National Institute of Mental Health 💵
-- B. Nolan Nichols 📖
-- Thomas E. Nichols 📖📢🔧
-- Dylan Nielson 📖💻🔧
-- Guiomar Niso 📖💡📢
-- Robert Oostenveld 📖🔧📢💡
-- Patrick Park 📖💡💬
-- Dianne Patterson 📖
-- John Pellman 📖
-- Cyril Pernet 💬📖💡📋
-- Franco Pestilli 📖
-- Dmitry Petrov 📖💻
-- Russell A. Poldrack 📖🔍📢
-- Jean-Baptiste Poline 📖📢🤔🎨
-- Vasudev Raguram 💻🎨📖🔧
-- Ariel Rokem 📖
-- Gunnar Schaefer 📖
-- Jan-Mathijs Schoffelen 📖
-- Vanessa Sochat 📖
-- Francois Tadel 📖🔌💡
-- Roberto Toro 🔧
-- William Triplett 📖
-- Jessica A. Turner 📖
-- Joseph Wexler 📖💡
-- Kirstie Whitaker 📖💡🔍🤔📢💬
-- Gaël Varoquaux 📖
-- Tal Yarkoni 💻📖🤔🔍🔌👀📢🐛🎨
+- Stefan Appelhoff 📖💬🤔🐛💡💻👀⚠️📢
+- Tibor Auer 💬📖💡🔧📢
+- Sylvain Baillet 📖🔍
+- Elizabeth Bock 📖💡
+- Eric Bridgeford 📖🔧
+- Teon L. Brooks 📖💻⚠️💬👀🤔🔧🐛📢
+- Suyash Bhogawar 📖💡⚠️🔧💬
+- Vince D. Calhoun 📖
+- Alexander L. Cohen 🐛💻📖💬
+- R. Cameron Craddock 📖📢
+- Samir Das 📖
+- Alejandro de la Vega 🐛💻⚠️
+- Arnaud Delorme 📖💡
+- Eugene P. Duff 📖
+- Elizabeth DuPre 📖💡🔍🤔
+- Eric A. Earl 🤔
+- Anders Eklund 📖📢💻
+- Oscar Esteban 📖🔧🤔💬💻
+- Franklin W. Feingold 📋📝✅
+- Guillaume Flandin 📖💻
+- Remi Gau 📖💻
+- Satrajit S. Ghosh 📖💻
+- Tristan Glatard 📖💻
+- Mathias Goncalves 💻🔧📢
+- Krzysztof J. Gorgolewski 📖💻💬🤔🔍📢📝💡🔌
+- Alexandre Gramfort 📖💡
+- Jeffrey S. Grethe 💬🐛✅📢
+- Yaroslav O. Halchenko 📖📢🔧💬🐛
+- Daniel A. Handwerker 📖
+- Michael Hanke 📖🤔🔧🐛📢
+- Michael P. Harms 📖⚠️🔧
+- Richard N. Henson 📖
+- Dora Hermes 📖💻✅🔍🤔
+- Katja Heuer 🔧
+- Chris Holdgraf 📖🤔
+- Jean-Christophe Houde 📖
+- International Neuroinformatics Coordinating Facility 💵📋
+- Mainak Jas 📖💻
+- David Keator 📖
+- James Kent 💬💻
+- Gregory Kiar 📖💻🎨🔧
+- Pamela LaMontagne 📖💡
+- Kevin Larcher 💬
+- Laura and John Arnold Foundation 💵
+- Xiangrui Li 📖💻
+- Vladimir Litvak 📖
+- Dan Lurie 🤔📖🔧🔌💻💬
+- Camille Maumet 📖
+- Christopher J. Markiewicz 💬📖💻
+- Jeremy Moreau 📖💡
+- Zachary Michael 📖
+- Ezequiel Mikulan 📖💻
+- Michael P. Milham 💡🔍
+- Henk Mutsaerts 📖
+- National Institute of Mental Health 💵
+- B. Nolan Nichols 📖
+- Thomas E. Nichols 📖📢🔧
+- Dylan Nielson 📖💻🔧
+- Guiomar Niso 📖💡📢
+- Robert Oostenveld 📖🔧📢💡✅⚠️🤔
+- Dimitri Papadopoulos Orfanos 📖💡🤔💬
+- Patrick Park 📖💡💬
+- Dianne Patterson 📖
+- John Pellman 📖
+- Cyril Pernet 💬📖💡📋
+- Franco Pestilli 📖
+- Dmitry Petrov 📖💻
+- Christophe Philips 📖
+- Russell A. Poldrack 📖🔍📢
+- Jean-Baptiste Poline 📖📢🤔🎨
+- Vasudev Raguram 💻🎨📖🔧
+- Ariel Rokem 📖
+- Matt Sanderson 📖💻
+- Gunnar Schaefer 📖
+- Jan-Mathijs Schoffelen 📖
+- Vanessa Sochat 📖
+- Francois Tadel 📖🔌💡
+- Roberto Toro 🔧
+- William Triplett 📖
+- Jessica A. Turner 📖
+- Joseph Wexler 📖💡
+- Kirstie Whitaker 📖💡🔍🤔📢💬
+- Gaël Varoquaux 📖
+- Tal Yarkoni 💻📖🤔🔍🔌👀📢🐛🎨
diff --git a/src/99-appendices/02-licenses.md b/src/99-appendices/02-licenses.md
index c6bd6bbf71..acc33aa34e 100644
--- a/src/99-appendices/02-licenses.md
+++ b/src/99-appendices/02-licenses.md
@@ -1,7 +1,12 @@
# Appendix II: Licenses
This section lists a number of common licenses for datasets and defines
-suggested abbreviations for use in the dataset metadata specifications
+suggested abbreviations for use in the dataset metadata specifications.
+
+Please note that this list only serves to provide some examples for possible
+licenses.
+The terms of any license should be consistent with the informed consent
+obtained from participants and any institutional limitations on distribution.
| Identifier | License name | Description |
| :--------- | :----------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index ced370f881..cb8d96539b 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -7,17 +7,18 @@ precede the reconstruction entity. REQUIRED and OPTIONAL entities for a given
file type are denoted. Entity formats indicate whether the value is alphanumeric
(``) or numeric (``).
-| Entity | Format | anat` | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED |
-| Session | `ses-` | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL |
-| Task | `task-` | | | REQUIRED | REQUIRED | | | | REQUIRED | REQUIRED | REQUIRED |
-| Acquisition | `acq-` | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | OPTIONAL | OPTIONAL |
-| Contrast Enhancing Agent | `ce-` | OPTIONAL | OPTIONAL | OPTIONAL | | | | OPTIONAL | | | |
-| Reconstruction | `rec-` | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | | | | | |
-| Phase-Encoding Direction | `dir-` | | | OPTIONAL | | OPTIONAL | | REQUIRED | | | |
-| Run | `run-` | | | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | OPTIONAL | OPTIONAL |
-| Corresponding modality | `mod-` | | OPTIONAL | | | | | | | | |
-| Echo | `echo-` | | | OPTIONAL | | | | | | | |
-| Recording | `recording-` | | | | OPTIONAL | | | | | | |
-| Processed (on device) | `proc-` | | | | OPTIONAL | | | | | OPTIONAL | OPTIONAL |
+| Entity | Format | anat` | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED |
+| Session | `ses-` | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL |
+| Task | `task-` | | | REQUIRED | REQUIRED | | | | REQUIRED | REQUIRED | REQUIRED | REQUIRED | REQUIRED | | OPTIONAL | | | REQUIRED |
+| Acquisition | `acq-` | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | OPTIONAL | OPTIONAL | OPTIONAL | | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | |
+| Contrast Enhancing Agent | `ce-` | OPTIONAL | OPTIONAL | OPTIONAL | | | | OPTIONAL | | | | | | | | | | |
+| Reconstruction | `rec-` | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | | | | | | | | | | | | |
+| Phase-Encoding Direction | `dir-` | | | OPTIONAL | | OPTIONAL | | REQUIRED | | | | | | | | | | |
+| Run | `run-` | | | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | | | | OPTIONAL |
+| Corresponding modality | `mod-` | | OPTIONAL | | | | | | | | | | | | | | | |
+| Echo | `echo-` | | | OPTIONAL | | | | | | | | | | | | | | |
+| Recording | `recording-` | | | | OPTIONAL | | | | | | | | | | | | | |
+| Processed (on device) | `proc-` | | | | OPTIONAL | | | | | OPTIONAL | | | | | | | | |
+| Space | `space-` | | | | | | | | | | | | | OPTIONAL | OPTIONAL | | OPTIONAL | |
diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index 7c475c47a7..7292e8eaf6 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -26,11 +26,11 @@ folder.
sub-[_ses-]_task-[_run-]_meg.ds>
```
-CTF’s data storage is therefore via directories containing multiple files. The
-files contained within a .ds directory are named such that they match the parent
-directory, but conserve the original file extension (e.g., `.meg4`, `.res4`,
-etc.). The renaming of CTF datasets SHOULD be done using the CTF newDs
-command-line application.
+CTF's data storage is therefore via directories containing multiple files. The
+files contained within a .ds directory are named such that they match the
+parent directory, but preserve the original file extension (e.g., `.meg4`,
+`.res4`, etc.). The renaming of CTF datasets SHOULD be done with a specialized
+software such as the CTF newDs command-line application or [MNE-BIDS](https://github.com/mne-tools/mne-bids).
Example:
@@ -155,12 +155,11 @@ More about the 4D neuroimaging/BTi data organization at:
## KIT/Yokogawa/Ricoh
-Each experimental run on a KIT/Yokogawa/Ricoh system yields a raw (`.sqd`,
-`.con`) file with its associated marker coil file (`.mrk`), which contains coil
-positions in the acquisition system’s native space. Head points and marker
-points in head space are acquired using third-party hardware. One SHOULD
-rename/create a father run specific directory and keep the original files for
-each run inside.
+Each experimental run on a KIT/Yokogawa/Ricoh system yields a raw
+(`.sqd`, `.con`) file with its associated marker coil file(s) (`.sqd`, `.mrk`),
+which contains coil positions in the acquisition system’s native space.
+Head points and marker points in head space are acquired using third-party
+hardware.
Example:
@@ -174,15 +173,16 @@ sub-control01/
sub-control01_ses-001_task-rest_run-01_meg
sub-control01_ses-001_task-rest_run-01_meg.json
sub-control01_ses-001_task-rest_run-01_channels.tsv
+ sub-control01_ses-001_task-rest[_acq-]_run-01_markers.
+ sub-control01_ses-001_task-rest_run-01_meg.
```
-Where:
-
-```Text
-sub-control01_ses-001_task-rest_run-01_meg/
- sub-control01_ses-001_task-rest_run-01_markers.
- sub-control01_ses-001_task-rest_run-01_meg.
-```
+If there are files with multiple marker coils, the marker files must have the
+`acq-` parameter and no more that two marker files may be associated with
+one raw data file.
+While the acquisition parameter can take any value, it is RECOMMENDED that if
+the two marker measurements occur before and after the raw data acquisition,
+`pre` and `post` are used to differentiate the two situations.
More about the KIT/Yokogawa/Ricoh data organization at:
[http://www.fieldtriptoolbox.org/getting_started/yokogawa](http://www.fieldtriptoolbox.org/getting_started/yokogawa)
@@ -213,15 +213,9 @@ sub-control01/
sub-control01_ses-001_task-rest_run-01_meg
sub-control01_ses-001_task-rest_run-01_meg.json
sub-control01_ses-001_task-rest_run-01_channels.tsv
-```
-
-Where:
-
-```Text
-sub-control01_ses-001_task-rest_run-01_meg/
- sub-control01_ses-001_task-rest_run-01_meg.chn
- sub-control01_ses-001_task-rest_run-01_meg.kdf
- sub-control01_ses-001_task-rest_run-01_meg.trg
+ sub-control01_ses-001_task-rest_run-01_meg.chn
+ sub-control01_ses-001_task-rest_run-01_meg.kdf
+ sub-control01_ses-001_task-rest_run-01_meg.trg
```
## ITAB
@@ -232,9 +226,7 @@ header that contains detailed information about the data acquisition system,
followed by binary data. The associated binary header file contains part of the
information from the ASCII header, specifically the one needed to process data,
plus other information on offline preprocessing performed after data acquisition
-(e.g., sensor position relative to subject’s head, head markers, stimulus
-information). One should rename/create a father run specific directory and keep
-the original files for each run inside.
+(e.g., sensor position relative to subject’s head, head markers, stimulus information).
Example:
@@ -246,14 +238,8 @@ sub-control01/
sub-control01_ses-001_task-rest_run-01_meg
sub-control01_ses-001_task-rest_run-01_meg.json
sub-control01_ses-001_task-rest_run-01_channels.tsv
-```
-
-Where:
-
-```Text
-sub-control01_ses-001_task-rest_run-01_meg/
- sub-control01_ses-001_task-rest_run-01_meg.raw
- sub-control01_ses-001_task-rest_run-01_meg.raw.mhd
+ sub-control01_ses-001_task-rest_run-01_meg.raw
+ sub-control01_ses-001_task-rest_run-01_meg.raw.mhd
```
## Aalto MEG–MRI
diff --git a/src/99-appendices/07-meg-systems.md b/src/99-appendices/07-meg-systems.md
index 3a04aae881..a8ae49880c 100644
--- a/src/99-appendices/07-meg-systems.md
+++ b/src/99-appendices/07-meg-systems.md
@@ -2,14 +2,14 @@
Restricted keywords for Manufacturer field in the `*meg.json` file:
-- `CTF`
-- [`Elekta/Neuromag`](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/edit#heading=h.a7ggx48p7aaf)
-- [`4D/BTi`](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/edit#heading=h.gy0kbzisg1f1)
-- [`KIT/Yokogawa/Ricoh`](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/edit#heading=h.2gmmxawyna7r)
-- `KRISS`
-- [`ITAB`](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/edit#heading=h.58whib3oq56y)
-- `Aalto/MEG–MRI`
-- `Other`
+- `CTF`
+- [`Elekta/Neuromag`](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/edit#heading=h.a7ggx48p7aaf)
+- [`4D/BTi`](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/edit#heading=h.gy0kbzisg1f1)
+- [`KIT/Yokogawa/Ricoh`](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/edit#heading=h.2gmmxawyna7r)
+- `KRISS`
+- [`ITAB`](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/edit#heading=h.58whib3oq56y)
+- `Aalto/MEG–MRI`
+- `Other`
Restricted keywords for ManufacturersModelName field in the `*meg.json` file:
diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md
index 3ee9e60937..674b20c0a0 100644
--- a/src/99-appendices/08-coordinate-systems.md
+++ b/src/99-appendices/08-coordinate-systems.md
@@ -1,4 +1,4 @@
-# Appendix VIII: preferred names of Coordinate systems
+# Appendix VIII: Preferred Names of Coordinate Systems
To interpret a coordinate (x, y, z), it is required that you know relative to
which origin the coordinates are expressed, you have to know the interpretation
@@ -7,7 +7,9 @@ expressed. This information is sometimes called the coordinate system.
These letters help describe the coordinate system definition:
-A/P means anterior/posterior L/R means left/right S/I means superior/inferior
+- A/P means anterior/posterior
+- L/R means left/right
+- S/I means superior/inferior
For example: `RAS` means that the first dimension (X) points towards the right
hand side of the head, the second dimension (Y) points towards the Anterior
@@ -16,7 +18,7 @@ head.
Besides coordinate systems, defined by their origin and direction of the axes,
BIDS defines "spaces" as an artificial frame of reference, created to describe
-different anatomies in a unifying manner (see e.g.
+different anatomies in a unifying manner (see e.g.,
[https://doi.org/10.1016/j.neuroimage.2012.01.024](https://www.sciencedirect.com/science/article/pii/S1053811912000419?via%3Dihub)).
The "space" and all coordinates expressed in this space are by design a
transformation of the real world geometry, and nearly always different from the
@@ -30,41 +32,41 @@ The coordinate systems below all relate to neuroscience and therefore to the
head or brain coordinates. Please be aware that all data acquisition starts with
"device coordinates" (scanner), which does not have to be identical to the
initial "file format coordinates" (DICOM), which are again different from the
-"head" coordinates (e.g. NIFTI). Not only do device coordinate vary between
+"head" coordinates (e.g., NIFTI). Not only do device coordinate vary between
hardware manufacturers, but also the head coordinates differ, mostly due to
different conventions used in specific software packages developed by different
(commercial or academic) groups.
-## MEG specific Coordinate Systems
+## Coordinate Systems applicable to MEG, EEG, and iEEG
-The first two pieces of information (origin, orientation) are specified in
-`XXXCoordinateSystem`, the units are specified in `XXXCoordinateSystemUnits`.
+Generally, across the MEG, EEG, and iEEG modalities, the first two pieces of
+information (origin, orientation) are specified in `XXXCoordinateSystem`, and
+the units are specified in `XXXCoordinateSystemUnits`.
-Restricted keywords for the XXXCoordinateSystem field in the
-`coordinatesystem.json` file for MEG datasets:
-
-- CTF: ALS orientation and the origin between the ears
-
-- ElektaNeuromag: RAS orientation and the origin between the ears
+Allowed values for the `XXXCoordinateSystem` field come from a list of
+restricted keywords, as listed in the sections below. If no value from the
+list of restricted keywords fits, there is always the option to specify the
+value as follows:
-- 4DBti: ALS orientation and the origin between the ears
+- `Other`: Use this for other coordinate systems and specify further details
+ in the `XXXCoordinateSystemDescription` field
-- KitYokogawa: ALS orientation and the origin between the ears
+## MEG Specific Coordinate Systems
-- ChietiItab: RAS orientation and the origin between the ears
-
-- Other: Use this for other coordinate systems and specify further details in
- the `XXXCoordinateSystemDescription` field
+Restricted keywords for the `XXXCoordinateSystem` field in the
+`coordinatesystem.json` file for MEG datasets:
-Note that the short descriptions above do not capture all details, there are
-detailed descriptions of these coordinate systems on the FieldTrip toolbox web
-page:
-[http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
+- `CTF`: ALS orientation and the origin between the ears
+- `ElektaNeuromag`: RAS orientation and the origin between the ears
+- `4DBti`: ALS orientation and the origin between the ears
+- `KitYokogawa`: ALS orientation and the origin between the ears
+- `ChietiItab`: RAS orientation and the origin between the ears
-## EEG specific Coordinate Systems
+Note that the short descriptions above do not capture all details, There are
+detailed extensive descriptions of these EEG coordinate systems on the
+[FieldTrip toolbox web page](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
-The first two pieces of information (origin, orientation) are specified in
-`XXXCoordinateSystem`, the units are specified in `XXXCoordinateSystemUnits`.
+## EEG Specific Coordinate Systems
Restricted keywords for the `XXXCoordinateSystem` field in the
`coordsystem.json` file for EEG datasets:
@@ -78,12 +80,31 @@ Restricted keywords for the `XXXCoordinateSystem` field in the
- `Captrak`: RAS orientation and the origin between the ears
Note that the short descriptions above do not capture all details, There are
-detailed extensive descriptions of these EEG coordinate systems on the FieldTrip
-toolbox web page and on the BESA wiki:
-[http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
-[http://wiki.besa.de/index.php?title=Electrodes_and_Surface_Locations\#Coordinate_systems](http://wiki.besa.de/index.php?title=Electrodes_and_Surface_Locations#Coordinate_systems)
+detailed extensive descriptions of these EEG coordinate systems on the
+[FieldTrip toolbox web page](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
+and on the [BESA wiki](http://wiki.besa.de/index.php?title=Electrodes_and_Surface_Locations#Coordinate_systems).
-## Template based Coordinate Systems
+## iEEG Specific Coordinate Systems
+
+Restricted keywords for the `XXXCoordinateSystem` field in the
+`coordsystem.json` file for iEEG datasets:
+
+- `Pixels`: If electrodes are localized in 2D space (only x and y are
+ specified and z is n/a), then the positions in this file must correspond to
+ the locations expressed in pixels on the photo/drawing/rendering of the
+ electrodes on the brain. In this case, coordinates must be (row,column)
+ pairs, with (0,0) corresponding to the upper left pixel and (N,0)
+ corresponding to the lower left pixel.
+
+- `ACPC`: The origin of the coordinate system is at the Anterior Commissure
+ and the negative y-axis is passing through the Posterior Commissure. The
+ positive z-axis is passing through a mid-hemispheric point in the superior
+ direction. The anatomical landmarks are determined in the individual's
+ anatomical scan and no scaling or deformations have been applied to the
+ individual's anatomical scan. For more information, see the [ACPC site](http://www.fieldtriptoolbox.org/faq/acpc/)
+ on the FieldTrip toolbox wiki.
+
+## Template Based Coordinate Systems
The transformation of the real world geometry to an artificial frame of
reference is described in `XXXCoordinateSystem`. Unless otherwise specified
diff --git a/src/CHANGES.md b/src/CHANGES.md
new file mode 100644
index 0000000000..ccb403abfb
--- /dev/null
+++ b/src/CHANGES.md
@@ -0,0 +1,278 @@
+Changelog
+
+## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
+
+- \[FIX] remove ManufacturersAmplifierModelName (again) [#236](https://github.com/bids-standard/bids-specification/pull/236) ([robertoostenveld](https://github.com/robertoostenveld))
+- \[INFRA] Update release protocol [#235](https://github.com/bids-standard/bids-specification/pull/235) ([effigies](https://github.com/effigies))
+- REL: 1.3.0-dev [#234](https://github.com/bids-standard/bids-specification/pull/234) ([effigies](https://github.com/effigies))
+- \[INFRA] Enable version panel for quickly finding previous versions [#232](https://github.com/bids-standard/bids-specification/pull/232) ([effigies](https://github.com/effigies))
+- \[FIX] use \\<label> for \_desc- - not some \\<value> + clarify \\<value> [#224](https://github.com/bids-standard/bids-specification/pull/224) ([yarikoptic](https://github.com/yarikoptic))
+- \[FIX] Clarify Appendix II: The list of licenses only lists examples [#222](https://github.com/bids-standard/bids-specification/pull/222) ([sappelhoff](https://github.com/sappelhoff))
+- \[FIX] Trivial column header fix [#220](https://github.com/bids-standard/bids-specification/pull/220) ([nicholst](https://github.com/nicholst))
+- \[INFRA] Add clarification on merge methods to DECISION_MAKING [#217](https://github.com/bids-standard/bids-specification/pull/217) ([sappelhoff](https://github.com/sappelhoff))
+- \[INFRA] Enable permalink urls to appear at (sub)section headings [#214](https://github.com/bids-standard/bids-specification/pull/214) ([yarikoptic](https://github.com/yarikoptic))
+- \[INFRA] bump up mkdocs-materials version [#211](https://github.com/bids-standard/bids-specification/pull/211) ([sappelhoff](https://github.com/sappelhoff))
+- \[ENH] Various proposed changes to diffusion derivatives [#205](https://github.com/bids-standard/bids-specification/pull/205) ([Lestropie](https://github.com/Lestropie))
+- \[MISC] Fix github username for @chrisgorgo [#204](https://github.com/bids-standard/bids-specification/pull/204) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[FIX] clarify example 3 in common principles (inheritance) [#202](https://github.com/bids-standard/bids-specification/pull/202) ([sappelhoff](https://github.com/sappelhoff))
+- \[MISC] Expand entity table for MEG/EEG/iEEG specific files [#198](https://github.com/bids-standard/bids-specification/pull/198) ([sappelhoff](https://github.com/sappelhoff))
+- \[FIX] make iEEG ToC more consistent with MEG and EEG [#191](https://github.com/bids-standard/bids-specification/pull/191) ([robertoostenveld](https://github.com/robertoostenveld))
+- \[FIX] Clarify use of acq and task parameters in EEG, MEG, and iEEG [#188](https://github.com/bids-standard/bids-specification/pull/188) ([sappelhoff](https://github.com/sappelhoff))
+- \[FIX] clarify use of tools for CTF data renaming [#187](https://github.com/bids-standard/bids-specification/pull/187) ([sappelhoff](https://github.com/sappelhoff))
+- \[MISC] Add bep006 and bep010 to completed beps and fix links [#186](https://github.com/bids-standard/bids-specification/pull/186) ([sappelhoff](https://github.com/sappelhoff))
+- \[FIX] change file for definition of electrical stimulation labels from \_electrodes.json to \_events.json [#185](https://github.com/bids-standard/bids-specification/pull/185) ([ezemikulan](https://github.com/ezemikulan))
+- \[ENH] relax ieeg channel name requirements of letters and numbers only [#182](https://github.com/bids-standard/bids-specification/pull/182) ([sappelhoff](https://github.com/sappelhoff))
+- \[FIX] make MEG section headings and ToC consistent to the EEG and iEEG specs [#181](https://github.com/bids-standard/bids-specification/pull/181) ([robertoostenveld](https://github.com/robertoostenveld))
+- \[FIX] make section headings and ToC consistent between meg and eeg specs [#180](https://github.com/bids-standard/bids-specification/pull/180) ([robertoostenveld](https://github.com/robertoostenveld))
+- \[MISC] Spelling fixes [#179](https://github.com/bids-standard/bids-specification/pull/179) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+- \[ENH] Alternative folder organization for raw, derived, and source data [#178](https://github.com/bids-standard/bids-specification/pull/178) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[INFRA] Adding instructions for naming PRs [#177](https://github.com/bids-standard/bids-specification/pull/177) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[MISC] Introducing Stefan Appelhoff as the first Maintainer [#176](https://github.com/bids-standard/bids-specification/pull/176) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[FIX] Clarify name of "BrainVision" format [#175](https://github.com/bids-standard/bids-specification/pull/175) ([JegouA](https://github.com/JegouA))
+- \[FIX] Fixes spelling of continuous [#171](https://github.com/bids-standard/bids-specification/pull/171) ([emdupre](https://github.com/emdupre))
+- \[FIX] Clarify continuous recording metadata fields [#167](https://github.com/bids-standard/bids-specification/pull/167) ([effigies](https://github.com/effigies))
+- \[FIX] changed reference of `dcm2nii` to `dcm2niix` [#166](https://github.com/bids-standard/bids-specification/pull/166) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+- \[FIX] Removing a leftover file [#162](https://github.com/bids-standard/bids-specification/pull/162) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[ENH] Derived (processed) MR data [#109](https://github.com/bids-standard/bids-specification/pull/109) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[FIX] Specify marker file names for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
+- \[FIX] Remove father-level for meg filetypes other than BTi/4D data [#19](https://github.com/bids-standard/bids-specification/pull/19) ([teonbrooks](https://github.com/teonbrooks))
+
+## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04)
+
+- REL: v1.2.0 [#161](https://github.com/bids-standard/bids-specification/pull/161) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+- RF: use "specification" not "protocol" to refer to BIDS [#156](https://github.com/bids-standard/bids-specification/pull/156) ([yarikoptic](https://github.com/yarikoptic))
+- Fix example misalignment [#155](https://github.com/bids-standard/bids-specification/pull/155) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+- Update Pipfile.lock [#144](https://github.com/bids-standard/bids-specification/pull/144) ([franklin-feingold](https://github.com/franklin-feingold))
+- \[MRG] clarify decimal sep and numerical notation convention [#143](https://github.com/bids-standard/bids-specification/pull/143) ([sappelhoff](https://github.com/sappelhoff))
+- \[MRG] clarify encoding of README, CHANGES, TSV, and JSON files [#140](https://github.com/bids-standard/bids-specification/pull/140) ([sappelhoff](https://github.com/sappelhoff))
+- Update site_name and release protocol [#137](https://github.com/bids-standard/bids-specification/pull/137) ([franklin-feingold](https://github.com/franklin-feingold))
+- BF: Example for IntendedFor was missing session indicator in the filename [#129](https://github.com/bids-standard/bids-specification/pull/129) ([yarikoptic](https://github.com/yarikoptic))
+- Add "part" keyword for mag/phase BOLD images (based on BEP001). [#128](https://github.com/bids-standard/bids-specification/pull/128) ([tsalo](https://github.com/tsalo))
+- Update to Release_Protocol.md [#126](https://github.com/bids-standard/bids-specification/pull/126) ([franklin-feingold](https://github.com/franklin-feingold))
+- Update tag naming convention [#123](https://github.com/bids-standard/bids-specification/pull/123) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[MRG] Merge bep006 and bep010 [#108](https://github.com/bids-standard/bids-specification/pull/108) ([sappelhoff](https://github.com/sappelhoff))
+- Adding formal decision-making rules [#104](https://github.com/bids-standard/bids-specification/pull/104) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[MRG] number of small corrections to the specification [#98](https://github.com/bids-standard/bids-specification/pull/98) ([robertoostenveld](https://github.com/robertoostenveld))
+
+## [v1.1.2](https://github.com/bids-standard/bids-specification/tree/v1.1.2) (2019-01-10)
+
+- REL: v.1.1.2 [#121](https://github.com/bids-standard/bids-specification/pull/121) ([chrisgorgo](https://github.com/chrisgorgo))
+- Update 01-contributors.md [#120](https://github.com/bids-standard/bids-specification/pull/120) ([oesteban](https://github.com/oesteban))
+- Global fields in data dictionaries [#117](https://github.com/bids-standard/bids-specification/pull/117) ([chrisgorgo](https://github.com/chrisgorgo))
+- Propose BEP026 MER [#116](https://github.com/bids-standard/bids-specification/pull/116) ([greydongilmore](https://github.com/greydongilmore))
+- Remove duplicate entries in MEG table [#113](https://github.com/bids-standard/bids-specification/pull/113) ([franklin-feingold](https://github.com/franklin-feingold))
+- Propose BEP025 MIDS [#110](https://github.com/bids-standard/bids-specification/pull/110) ([josator2](https://github.com/josator2))
+- repair links [#106](https://github.com/bids-standard/bids-specification/pull/106) ([sappelhoff](https://github.com/sappelhoff))
+- Autogenerate CHANGES.md [#103](https://github.com/bids-standard/bids-specification/pull/103) ([franklin-feingold](https://github.com/franklin-feingold))
+- Added contributor information [#100](https://github.com/bids-standard/bids-specification/pull/100) ([jgrethe](https://github.com/jgrethe))
+- ENH: First(?) good practice recommendation. No excessive overrides in Inheritance principle [#99](https://github.com/bids-standard/bids-specification/pull/99) ([yarikoptic](https://github.com/yarikoptic))
+- adding extensions page [#97](https://github.com/bids-standard/bids-specification/pull/97) ([choldgraf](https://github.com/choldgraf))
+- Fix up some urls (as detected to be broken/inconsistent [#95](https://github.com/bids-standard/bids-specification/pull/95) ([yarikoptic](https://github.com/yarikoptic))
+- Change BEP numbers to include MRS [#94](https://github.com/bids-standard/bids-specification/pull/94) ([Hboni](https://github.com/Hboni))
+- RF harmonize and thus shorten templates etc [#93](https://github.com/bids-standard/bids-specification/pull/93) ([yarikoptic](https://github.com/yarikoptic))
+- put links and some text into README [#91](https://github.com/bids-standard/bids-specification/pull/91) ([sappelhoff](https://github.com/sappelhoff))
+- Add extension proposal in 01-introduction.md [#88](https://github.com/bids-standard/bids-specification/pull/88) ([Hboni](https://github.com/Hboni))
+- additional table to recap 'volume acquisition timing' [#87](https://github.com/bids-standard/bids-specification/pull/87) ([Remi-Gau](https://github.com/Remi-Gau))
+- Small typo in "scanning sequence" DICOM tag [#84](https://github.com/bids-standard/bids-specification/pull/84) ([Remi-Gau](https://github.com/Remi-Gau))
+- Update 01-contributors.md [#83](https://github.com/bids-standard/bids-specification/pull/83) ([teonbrooks](https://github.com/teonbrooks))
+- Added CBV contrast [#82](https://github.com/bids-standard/bids-specification/pull/82) ([TheChymera](https://github.com/TheChymera))
+- Add CC-BY 4.0 license [#81](https://github.com/bids-standard/bids-specification/pull/81) ([KirstieJane](https://github.com/KirstieJane))
+- Fix Travis break [#80](https://github.com/bids-standard/bids-specification/pull/80) ([franklin-feingold](https://github.com/franklin-feingold))
+- ENH: allow \_dir for other EPI (func, dwi) sequences [#78](https://github.com/bids-standard/bids-specification/pull/78) ([yarikoptic](https://github.com/yarikoptic))
+- Added appendix to mkdocs and added some internal links [#77](https://github.com/bids-standard/bids-specification/pull/77) ([franklin-feingold](https://github.com/franklin-feingold))
+- DOC: added JC Houde as contributor. [#76](https://github.com/bids-standard/bids-specification/pull/76) ([jchoude](https://github.com/jchoude))
+- Updated my contributions [#75](https://github.com/bids-standard/bids-specification/pull/75) ([nicholst](https://github.com/nicholst))
+- update HED appendix [#74](https://github.com/bids-standard/bids-specification/pull/74) ([sappelhoff](https://github.com/sappelhoff))
+- \[MRG] unicode: replace greek mu and omega by micro and ohm signs [#73](https://github.com/bids-standard/bids-specification/pull/73) ([sappelhoff](https://github.com/sappelhoff))
+- Update 01-contributors.md [#72](https://github.com/bids-standard/bids-specification/pull/72) ([francopestilli](https://github.com/francopestilli))
+- add ce-\\<label> for fmri data [#70](https://github.com/bids-standard/bids-specification/pull/70) ([dasturge](https://github.com/dasturge))
+- pin pip version [#68](https://github.com/bids-standard/bids-specification/pull/68) ([chrisgorgo](https://github.com/chrisgorgo))
+- Fix link in index [#46](https://github.com/bids-standard/bids-specification/pull/46) ([chrisgorgo](https://github.com/chrisgorgo))
+- edit contributing md [#44](https://github.com/bids-standard/bids-specification/pull/44) ([Park-Patrick](https://github.com/Park-Patrick))
+- Mkdocs configuration and RTD setup [#42](https://github.com/bids-standard/bids-specification/pull/42) ([choldgraf](https://github.com/choldgraf))
+- Move definitions, compulsory, and raw/derivatives sections to principles [#40](https://github.com/bids-standard/bids-specification/pull/40) ([chrisgorgo](https://github.com/chrisgorgo))
+- Remove duplicate section [#39](https://github.com/bids-standard/bids-specification/pull/39) ([chrisgorgo](https://github.com/chrisgorgo))
+- mkdocs rendering [#36](https://github.com/bids-standard/bids-specification/pull/36) ([chrisgorgo](https://github.com/chrisgorgo))
+- Style consistency [#35](https://github.com/bids-standard/bids-specification/pull/35) ([chrisgorgo](https://github.com/chrisgorgo))
+- Renaming files to conform with style guide [#34](https://github.com/bids-standard/bids-specification/pull/34) ([chrisgorgo](https://github.com/chrisgorgo))
+- enable travis cache [#32](https://github.com/bids-standard/bids-specification/pull/32) ([chrisgorgo](https://github.com/chrisgorgo))
+- FIX - corrected link that is shown for CC0 [#31](https://github.com/bids-standard/bids-specification/pull/31) ([robertoostenveld](https://github.com/robertoostenveld))
+- \[WIP] added linter integration via travis [#30](https://github.com/bids-standard/bids-specification/pull/30) ([chrisgorgo](https://github.com/chrisgorgo))
+- Cleanup [#29](https://github.com/bids-standard/bids-specification/pull/29) ([chrisgorgo](https://github.com/chrisgorgo))
+- \[MRG] split intro, commons, mr, and meg into folder from specification.md [#28](https://github.com/bids-standard/bids-specification/pull/28) ([teonbrooks](https://github.com/teonbrooks))
+- Add some bids starter kit contributors [#27](https://github.com/bids-standard/bids-specification/pull/27) ([KirstieJane](https://github.com/KirstieJane))
+- Embedded footnotes into text [#25](https://github.com/bids-standard/bids-specification/pull/25) ([franklin-feingold](https://github.com/franklin-feingold))
+- Making HED Strategy Guide link prettier [#24](https://github.com/bids-standard/bids-specification/pull/24) ([fake-filo](https://github.com/fake-filo))
+- Fix/more cleanup [#21](https://github.com/bids-standard/bids-specification/pull/21) ([chrisgorgo](https://github.com/chrisgorgo))
+- formatted MEG (8.4) [#17](https://github.com/bids-standard/bids-specification/pull/17) ([franklin-feingold](https://github.com/franklin-feingold))
+- small fixes [#16](https://github.com/bids-standard/bids-specification/pull/16) ([chrisgorgo](https://github.com/chrisgorgo))
+- Add meg img [#14](https://github.com/bids-standard/bids-specification/pull/14) ([sappelhoff](https://github.com/sappelhoff))
+- \[WIP] Cleaning up the specification [#13](https://github.com/bids-standard/bids-specification/pull/13) ([chrisgorgo](https://github.com/chrisgorgo))
+- Adding code of conduct [#6](https://github.com/bids-standard/bids-specification/pull/6) ([chrisgorgo](https://github.com/chrisgorgo))
+- Renaming the main document [#1](https://github.com/bids-standard/bids-specification/pull/1) ([chrisgorgo](https://github.com/chrisgorgo))
+
+## 1.1.1
+
+- Improved the MEG landmark coordinates description.
+
+- Replaced ManufacturersCapModelName in meg.json with CapManufacturer and
+ CapManufacturersModelName.
+
+- Remove EEGSamplingFrequency and ManufacturersAmplifierModelName
+ from the meg.json.
+
+- Improved the behavioral data description.
+
+## 1.1.0
+
+- Added support for MEG data (merged BEP008)
+- Added SequenceName field.
+- Added support for describing events with Hierarchical Event Descriptors \[[4.3 Task events](04-modality-specific-files/05-task-events.md)].
+- Added VolumeTiming and AcquisitionDuration fields \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+- Added DwellTime field.
+
+## 1.0.2
+
+- Added support for high resolution (anatomical) T2star images \[[4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)].
+
+- Added support for multiple defacing masks \[[4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)].
+
+- Added optional key and metadata field for contrast enhanced structural scans
+ \[[4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]
+
+- Added DelayTime field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+- Added support for multi echo BOLD data \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+## 1.0.1
+
+- Added InstitutionName field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+- Added InstitutionAddress field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+- Added DeviceSerialNumber field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+- Added NumberOfVolumesDiscardedByUser and
+ NumberOfVolumesDiscardedByScanner field \[[4.1 Task (including
+ resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+- Added TotalReadoutTime to functional images metadata list
+ \[[4.1 Task (including resting state) imaging
+ data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
+
+## 1.0.1-rc1
+
+- Added T1 Rho maps \[[4.1 Anatomy imaging
+ data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)].
+
+- Added support for phenotypic information split into multiple files
+ \[[3.2 Participant key file](03-modality-agnostic-files.md#participants-file)].
+
+- Added recommendations for multi site datasets
+
+- Added SoftwareVersions
+
+- Added run-<run_index> to the phase encoding
+ maps. Improved the description.
+
+- Added InversionTime metadata key.
+
+- Clarification on the source vs raw language.
+
+- Added trial_type column to the event files.
+
+- Added missing sub-<participant_label> in
+ behavioral data file names
+
+- Added ability to store stimuli files.
+
+- Clarified the language describing allowed subject labels.
+
+- Added quantitative proton density maps.
+
+## 1.0.0
+
+- Added ability to specify fieldmaps acquired with multiple parameter
+ sets.
+
+- Added ability to have multiple runs of the same fieldmap.
+
+- Added FLASH anatomical images.
+
+## 1.0.0-rc4
+
+- Replaced links to neurolex with explicit DICOM Tags.
+
+- Added sourcedata.
+
+- Added data dictionaries.
+
+- Be more explicit about contents of JSON files for structural
+ (anatomical) scans.
+
+## 1.0.0-rc3
+
+- Renamed PhaseEncodingDirection values from “x”, “y”,
+ “z” to “i”, “j”, “k” to avoid confusion with FSL parameters
+
+- Renamed SliceEncodingDirection values from “x”, “y”,
+ “z” to “i”, “j”, “k”
+
+## 1.0.0-rc2
+
+- Removed the requirement that TSV files cannot include more than two
+ consecutive spaces.
+
+- Refactor of the definitions sections (copied from the
+ manuscript)
+
+- Make support for uncompressed .nii files more explicit.
+
+- Added BIDSVersion to dataset.json
+
+- Remove the statement that SliceEncodingDirection is
+ necessary for slice time correction
+
+- Change dicom converter recommendation from dcmstack to dcm2nii and
+ dicm2nii following interactions with the community (see
+ and
+ ).
+
+- Added section on behavioral experiments with no accompanying MRI
+ acquisition
+
+- Add \_magnitude.nii\[.gz] image for GE type
+ fieldmaps.
+
+- Replaced EchoTimeDifference with
+ EchoTime1 and EchoTime2 (SPM toolbox
+ requires this input).
+
+- Added support for single band reference image for DWI.
+
+- Added DatasetDOI field in the dataset
+ description.
+
+- Added description of more metadata fields relevant to DWI fieldmap
+ correction.
+
+- PhaseEncodingDirection is now expressed in “x”, “y” etc. instead of “PA”
+ “RL” for DWI scans
+ (so it’s the same as BOLD scans)
+
+- Added rec-<label> flag to BOLD files to
+ distinguish
+ between different reconstruction algorithms
+ (analogous to anatomical scans).
+
+- Added recommendation to use \_physio suffix for continuous recordings
+ of motion
+ parameters obtained by
+ the scanner side reconstruction algorithms.
+
+## 1.0.0-rc1
+
+- Initial release
+
+\* _This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)_
diff --git a/src/js/jquery-3.4.1.min.js b/src/js/jquery-3.4.1.min.js
new file mode 100644
index 0000000000..a1c07fd803
--- /dev/null
+++ b/src/js/jquery-3.4.1.min.js
@@ -0,0 +1,2 @@
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