diff --git a/README.md b/README.md index 7db8b83faa..e01c6f2c66 100644 --- a/README.md +++ b/README.md @@ -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 diff --git a/src/01-introduction.md b/src/01-introduction.md index fe0f66b676..653c01fabe 100644 --- a/src/01-introduction.md +++ b/src/01-introduction.md @@ -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 diff --git a/src/06-extensions.md b/src/06-extensions.md index 8bc05e014b..e928365481 100644 --- a/src/06-extensions.md +++ b/src/06-extensions.md @@ -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). -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.