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chrisgorgo committed Mar 20, 2019
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2 changes: 1 addition & 1 deletion CODEOWNERS
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Validating CODEOWNERS rules …
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# 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
# Add your GitHub name below to get notified about proposed releases
/src/CHANGES.md @chrisfilo @sappelhoff @CPernet

# Individual sections
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8 changes: 4 additions & 4 deletions CONTRIBUTING.md
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Expand Up @@ -44,7 +44,7 @@ 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 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.

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#### 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.
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
Expand All @@ -109,11 +109,11 @@ Use one of the following prefixes in the title of your pull request:

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 [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
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.

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23 changes: 20 additions & 3 deletions DECISION-MAKING.md
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Expand Up @@ -25,6 +25,15 @@ community decides on the content of this file using the same process as any
other change to the Repository (see below) allowing the meaning of "Contributor"
to evolve independently of the Decision-making rules.

**Maintainer** - a Contributor responsible for the long term health of the
project and the community. Maintainers have additional rights (see Rules)
helping them to resolve conflicts and increase the pace of the development
when necessary. Current Maintainers:

| Name | Time commitment |
|-----------------------------------------------------------------|-----------------|
| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff)) | 5h/week |

## Rules

1. Every modification of the specification (including a correction of a typo,
Expand All @@ -45,6 +54,11 @@ to evolve independently of the Decision-making rules.
1. Does not feature any [Reviews that Request changes](https://help.github.com/articles/about-required-reviews-for-pull-requests/).
1. Does not feature "WIP" in the title (Work in Progress).
1. Passes all automated tests.
1. Is not proposing a new release or has been approved by at least one
Maintainer (i.e., PRs proposing new releases need to be approved by at
least one Maintainer).
1. A Maintainer can merge any PR - even if it's not eligible to merge according
to Rule 4.
1. Any Contributor can Review a PR and Request changes. If a Contributor
Request changes they need to provide an explanation what changes
should be added and justification of their importance. Reviews requesting
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1. If the author of a PR and Contributor who provided Review that Requests
changes cannot find a solution that would lead to the Contributor dismissing
their review or accepting the changes the Review can be Dismissed with a
vote. Rules governing voting:
vote or by a Maintainer. Rules governing voting:
1. A Vote can be triggered by any Contributor, but only after 5 working days
from the time a Review Requesting Changes has been raised and in case a
Vote has been triggered previously no sooner than 15 working days since
Expand All @@ -70,13 +84,16 @@ to evolve independently of the Decision-making rules.

## Comments

1. Researchers preparing academic manuscripts describing work that has been
merged into this repository are strongly encouraged to invite all
Maintainers as co-authors as a form of appreciation for their work.
1. There are no restrictions on how the content of the PR is prepared. For
example it is perfectly fine for a PR to consist of content developed by a
group of experts over an extended period of time via in person meetings and
online collaborations using a Google Document.
1. To facilitate triaging of incoming PR you can subscribe to
1. To facilitate triage of incoming PR you can subscribe to
notifications for new PRs proposing changes to specific files. To do this
add your Github name next to the file you want to subscribe to in the
add your GitHub name next to the file you want to subscribe to in the
[CODEOWNERS](CODEOWNERS). This way you will be ask to review each relevant
PR. Please mind that lack of your review will not prevent the PR from being
merged so if you think the PR needs your attention, please review it
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2 changes: 1 addition & 1 deletion Release_Protocol.md
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Expand Up @@ -19,7 +19,7 @@ Important note: The pull request title **needs** to follow this protocol. REL: v

### This will open a period of discussion for 5 business days regarding if we are ready to release. This will also freeze all pull request merging.

If we determine we are ready to release, please have the PR submitter add an additional commit with the date in year-month-date format in parentheses after the version of the date of merging (not opening) (i.e. it should read v1.1.2 (2018-12-28)) and merge this PR. This will mark a new release. On the same day, please also do a github release. To do this please see below.
If we determine we are ready to release, please have the PR submitter add an additional commit with the date in year-month-date format in parentheses after the version of the date of merging (not opening) (i.e. it should read v1.1.2 (2018-12-28)) and merge this PR. This will mark a new release. On the same day, please also do a GitHub release. To do this please see below.

![GH-release-1](release_images/GH-release_1.png "GH-release-1")

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4 changes: 2 additions & 2 deletions pull_request_template.md
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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 [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/)
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 ---
--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---
2 changes: 1 addition & 1 deletion src/01-introduction.md
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Expand Up @@ -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).
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23 changes: 23 additions & 0 deletions src/02-common-principles.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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| 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 |
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1 change: 1 addition & 0 deletions src/CHANGES.md
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Expand Up @@ -2,6 +2,7 @@ Changelog

## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)

- \[MISC] Introducing Stefan Appelhoff as the first Maintainer [#176](https://github.com/bids-standard/bids-specification/pull/176) ([chrisfilo](https://github.com/chrisfilo))
- \[FIX] Fixes spelling of continuous [#171](https://github.com/bids-standard/bids-specification/pull/171) ([emdupre](https://github.com/emdupre))
- \[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) ([chrisfilo](https://github.com/chrisfilo))
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