Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[MISC] moved list of extension proposals to the main BIDS website #389

Merged
merged 1 commit into from
Jan 15, 2020
Merged

[MISC] moved list of extension proposals to the main BIDS website #389

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 1 addition & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,7 @@ To organize your data in BIDS, all you need is neuro data, a computer, and the
[BIDS specification](https://bids-specification.readthedocs.io/en/stable/).

BIDS currently supports MRI, MEG, EEG, iEEG, behavioral, and physiological data
and more modalities are being added continuously (see here for
[work in progress modalities](https://bids-specification.readthedocs.io/en/stable/06-extensions.html#bids-extension-proposals)).
and more modalities will be added.

# Formatting your data with BIDS

Expand Down
3 changes: 1 addition & 2 deletions src/01-introduction.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,8 +46,7 @@ different backgrounds.

The BIDS specification can be extended in a backwards compatible way and will
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
Proposals (BEPs). For more information about the BEP process, see
[Extending the BIDS specification](06-extensions.md).

## Citing BIDS
Expand Down
69 changes: 3 additions & 66 deletions src/06-extensions.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,71 +1,8 @@
# Contributing to and extending the BIDS specification

This page lists some ways that you can get involved with the BIDS community.

## Contributing to BIDS

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).
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

are you going to remove the BIDS Starter Kit dropdown menu as well?
image

On the website and in your updating PR (bids-standard/bids-website#77), I don't see a reference to the starter kit yet - perhaps it'd be good to add it somewhere.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The starter kit is already mentioned on the website under https://bids.neuroimaging.io/getting_started.html.

Although I did not make the initial section headings - just copied them - I suppose that "getting started" on the main website is more aimed towards users and "get involved" more at developers/contributors. The distinction between the two is ideally not very strict, since everyone would contribute one way or another to the BIDS ecosystem (with data, knowledge, insights, skills, technical effort, etc).

On the bids-specification site on RTD, the starter kit was not only mentioned on https://bids-specification.readthedocs.io/en/stable/06-extensions.html (even though the starter kit does not really deal with how to work on BEPs), but also still features in the top-level menu that appears on the left of the screen.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Oh, I now see your 1st question:

are you going to remove the BIDS Starter Kit dropdown menu as well?

If it is up to me, yes. But I think that should be a separate PR on both sides, so this PR keeps that as is. We first might want to improve the way how the Starter Kit is featured on the main website. And perhaps even reconsider the current Starter Kit implementation altogether.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Okay, that's a good way to move forward.

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).
It contains more in-depth information for getting involved with the BIDS
community.

## BIDS Extension Proposals
# BIDS Extension Proposals

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. The "Extension label" column
provides a direct link to the documentation.

| Extension label | Title | Moderators/ leads | Summary | Blocking point(s) |
| :---------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------- |
| [BEP001](https://github.com/bids-standard/bep001) | Structural acquisitions that include multiple contrasts (multi echo, flip angle, inversion time) sequences | Gilles de Hollander and Kirstie Whitaker | The draft BEP is nearly ready to be submitted as a PR. | A few items need to be revised and a final decision made. |
| [BEP002](https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M) | The BIDS Models Specification | Tal Yarkoni | Working with the computational models group for consistency. Starting with fMRI then extend to other modalities. | An item that is blocking progress is transformed data. |
| [BEP003](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4) | Common Derivatives | Available | Need a leader to help finish push this to completion. | An item that is blocking progress is coordinate systems. |
| [BEP004](https://docs.google.com/document/d/1kyw9mGgacNqeMbp4xZet3RnDhcMmf4_BmRgKaOkO2Sc) | Susceptibility Weighted Imaging (SWI) | Available | Looking for a new leader. | Searching for a new leader. |
| [BEP005](https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c) | Arterial Spin Labeling (ASL) | Henk-Jan Mutsaerts and Michael Chappell | Very close to completion. This includes finalizing the implementation in the validator and drafting the manuscript. | None. |
| [BEP009](https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0) | Positron Emission Tomography (PET) | Melanie Ganz | Very close to completion. This includes finalizing the standard and writing the paper. | None. |
| [BEP011](https://docs.google.com/document/d/1YG2g4UkEio4t_STIBOqYOwneLEs1emHIXbGKynx7V0Y) | The structural preprocessing derivatives | Andrew Hoopes | Have finalized the surface-based and volumetric overlays (and stats), differentiate between discrete and probabilistic segmentation. The next step for this BEP is standardizing the universal look-up table and characterizing surfaces. | None. |
| [BEP012](https://docs.google.com/document/d/16CvBwVMAs0IMhdoKmlmcm3W8254dQmNARo-7HhE-lJU) | The functional preprocessing derivatives | Camille Maumet and Chris Markiewicz | | None. |
| [BEP013](https://docs.google.com/document/d/1qBNQimDx6CuvHjbDvuFyBIrf2WRFUOJ-u50canWjjaw) | The resting state fMRI derivatives | Steven Giavasis | Merged into BEP012 | None. |
| [BEP014](https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE) | The affine transformations and nonlinear field warps | Oscar Esteban | A new file format (X5) to store spatial transforms is being created, and a draft proposal has been discussed under the scope of this BEP. A software prototype demonstrating X5 is currently under development. | In progress. |
| [BEP015](https://docs.google.com/document/d/1WYOTXDB7GzlHoWqLjd45I3uGBgPxXddST-NTqBnroJE) | Mapping file | Eric Earl, Camille Maumet, and Vasudev Raguram | Comments in BEP suggest this could be a tool rather than a BEP. This BEP is looking for thoughts and contributions. | Thoughts and contributions. |
| [BEP016](https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60) | The diffusion weighted imaging derivatives | Franco Pestilli and Oscar Esteban | Being discussed in a [GitHub repository](https://github.com/bids-standard/bids-bep016) | |
| [BEP017](https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA) | Generic BIDS connectivity data schema | Eugene Duff and Paul McCarthy | This BEP is searching for a reviewer with fresh eyes that understands the scope of this BEP. | None. |
| [BEP018](https://docs.google.com/document/d/1uRkgyzESLKuGjXi98Z97Wh6vt-iLN5nOAb9TG16CjUs) | Genetic information | Cyril R Pernet, Clara Moreau, and Thomas Nichols | Submitted a [pull request](https://github.com/bids-standard/bids-specification/pull/287) for review | None. |
| [BEP019](https://docs.google.com/document/d/1FqJI791ycXr0bfRg2qyLqAf0RpVttJ2cInOgMWrKsNU) | DICOM Metadata | Satrajit Ghosh | Not active - perhaps this is in the 20% of use cases. Could be a NIDM extension rather than in BIDS. | None. |
| [BEP020](https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw) | Eye Tracking including Gaze Position and Pupil Size(ET) | Benjamin Gagl and Dejan Draschkow | BEP is progressing and reaching consensus on items. | Small issues are blocking completion. |
| [BEP021](https://docs.google.com/document/d/1PmcVs7vg7Th-cGC-UrX8rAhKUHIzOI-uIOh69_mvdlw) | Common Electrophysiological Derivatives | Mainak Jas, Stefan Appelhoff, Cyril Pernet, Robert Oostenveld | Work has resumed since merging in EEG and iEEG. Next steps are to distribute a survey to gather what derivatives researchers care about, create example datasets to understand practical issues, and updates to the validator. | A few blocking items is what file format may be best suited and annotations. |
| [BEP022](https://docs.google.com/document/d/1pWCb02YNv5W-UZZja24fZrdXLm4X7knXMiZI7E2z7mY) | Magnetic Resonance Spectroscopy (MRS) | Dickson Wong | This is stalled effort, but trying to restart. | Restarting the effort. |
| [BEP023](https://docs.google.com/document/d/1yzsd1J9GT-aA0DWhdlgNr5LCu6_gvbjLyfvYq2FuxlY) | PET Preprocessing derivatives | Martin Noergaard, Graham Searle, Melanie Ganz | Work is paused until BEP009 manuscript has been submitted/accepted. | A blocking item is the need for more contributors, especially from senior PET experts. |
| [BEP024](https://docs.google.com/document/d/1fqnJZ18x5LJC8jiJ8yvPHUGFzNBZ6gW2kywYrUKWtuo) | Computed Tomography scan (CT) | Hugo Boniface | This effort has stalled and looking for more contributors and experts. | None. |
| [BEP025](https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4) | Medical Population Imaging Data structure (MIDS) | Jose Manuel Saborit Torres, Maria de la Iglesia Vayá | This BEP is working on the automated recognition of the DICOM sequence and writing the manuscript. | None. |
| [BEP026](https://docs.google.com/document/d/14KC1d5-Lx-7ZSMtwS7pVAAvz-2WR_uoo5FvsNirzqJw) | Microelectrode Recordings (MER) | Greydon Gilmore | Active effort. Looking for thoughts and contributions | None. |
| [BEP027](https://docs.google.com/document/d/104HLZedFtx0TaXEUwd7eyWvJUlc0CcSUtCzwjNgmGxE) | BIDS Execution | Chris Markiewicz and Greg Kiar | Partial draft seeking community input and fleshing out of some details. Examples and tooling should be available prior to release to demonstrate viability. | None. |

When an extension reaches maturity it is merged into the main body of the
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 |
| [BEP007](https://docs.google.com/document/d/1gs7USIVO1OApZs3IVo6TeXw9_tfzxhjM2-m--ex4g6o) | Hierarchical Event Descriptor (HED) Tags | Chris Gorgolewski |
| [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).
On the [BIDS homepage](https://bids.neuroimaging.io/) you can find a list of
extension protocols that are currently being worked on.