The BIDS community is preparing to merge the BIDS Extension Proposal 30 (BEP030) for Near Infrared Spectroscopy (NIRS). The updated draft is available for review at:
https://bids-specification.readthedocs.io/en/bep030/04-modality-specific-files/11-functional-near-infrared-spectroscopy.html
Note that the content of that HTML page may change as suggestions are accepted during the review process.
Comments and suggestions may be submitted on GitHub at:
bids-standard:master ← bids-standard:bep030
opened 10:51AM - 22 May 21 UTC
BEP030: Functional Near-Infrared Spectroscopy
This PR adds functional near-infr… ared spectroscopy to BIDS.
Leads: @rob-luke & @lpollonini
- validator: https://github.com/bids-standard/bids-validator/pull/952
- example: https://github.com/bids-standard/bids-examples/pull/305
- rendered specification draft: https://bids-specification.readthedocs.io/en/bep030/04-modality-specific-files/11-functional-near-infrared-spectroscopy.html
Progress:
- [x] Community reviewed proposal ([google docs](https://docs.google.com/document/d/1FzPt7TVpIAtlhrF9_9b2VBCZOrRXJASEMyHndhDQKl8/edit?ts=5f589efa#heading=h.nxhqi3lai5gs))
- [x] Transition google doc to markdown (this PR). [View current render here](https://bids-specification.readthedocs.io/en/bep030/04-modality-specific-files/11-functional-near-infrared-spectroscopy.html).
- [x] Fix language in document. It currently reads as if it was written by many people (as it was), and needs to be reworked to fix sentence structure and grammar.
- [x] Extend validator to support this BEP (WIP: [GitHub PR link](https://github.com/bids-standard/bids-validator/pull/952))
- [x] Generate open datasets from several labs and ensure they are compliant with specification (e.g. [dataset from rob-luke](https://github.com/rob-luke/BIDS-NIRS-Tapping), [dataset from robertoostenveld](http://www.fieldtriptoolbox.org/example/bids_nirs/), these are listed in the manuscript)
- [x] Add example dataset to [bids-examples](https://github.com/bids-standard/bids-examples) ([dataset 1](https://github.com/bids-standard/bids-examples/pull/305), [dataset 2](https://github.com/bids-standard/bids-examples/pull/323))
- [ ] Preprint of the new extension (manuscript hs been reviewed by half the authors, about to be circulated to remaining authors).
- [ ] Press release
NOTE: At all stages in this process we will actively advertise and invite feedback on the proposal. We invite all feedback no matter how minor or major. And we will advertise the draft website to the community for review once it is rendering correctly.
closes #438
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Scope of proposal:
This specification applies to the storage of raw fNIRS data and metadata, and does not address data processing or the storage of processed data. This specification aims to deal with data from well established commercial systems, not experimental or DIY systems, although everyone is encouraged to adhere to BIDS-fNIRS to facilitate future data sharing. The specification currently only addresses continuous wave (CW) fNIRS devices, but consideration is taken not to preclude extensions to TD and FD instruments in the future upon contributions from experts in these domains.
Considerations when reviewing this BEP:
* It was decided to only include continuous wave (CW) fNIRS in this BEP. However, we have taken effort not to preclude expansion to other techniques such as time or frequency domain fNIRS. We ask that TD and FD experts still review this proposal to ensure nothing in the specification precludes future expansion to other fNIRS types.
* This BEP does not specify details about hyper scanning, which is popular in the fNIRS community. This was decided as hyper scanning is not specific to fNIRS and is also performed using other modalities. Thus, hyper scanning should be added to BIDS in a modality agnostic manner. Hyperscanning is an open issue in BIDS (https://github.com/bids-standard/bids-specification/issues/402).
* A conscious decision was made not to specify what should be considered a short channel. The specification contains fields to store the number of short channels, as this will be important for searchability. But the definition of what exactly constitutes a short channel (is it less than 8mm, or 10mm, etc) is left to the end user and software packages.
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To provide feedback:
1. Select `Files Changed` in the tab list at the top of this text box.
2. Press the `Load Diff` button for the `src/04-modality-specific-files/10-functional-near-infrared-spectroscopy.md` file
3. Hover your mouse over any line that you wish to comment on, this should make a blue cross appear to the right of the line.
4. Press the blue cross and provide enter your comment
The community review will close on Wednesday (Sept 14th) at 23:59 UTC.
If no larger issues occur, all open comments and suggestions will be resolved in the following days and merged into the BEP. Afterwards, the BEP will be merged into the BIDS specification, followed by a 5-business-day long feature freeze and the release of BIDS 1.8.0 (then containing NIRS as a modality, among several more minor changes as documented in the BIDS changelog).
For more details on the release protocol, please see:
# Release Procedure
When it is time to release, use a pull request to put the repository into a releasable state,
allowing testing and edits prior to merging to master.
The following procedure ensures a predictable release.
The protocol assumes that you have a [fork](https://help.github.com/en/articles/fork-a-repo)
of the bids-standard/bids-specification repository and have [cloned](https://help.github.com/en/articles/cloning-a-repository)
your fork locally to a directory called `bids-specification`.
NOTE: Before you start a release, you have to ensure that the automatically generated changelog is
**up to date**. See the relevant [section in CONTRIBUTING.md](CONTRIBUTING.md#how-is-the-changelog-generated)
for further information. In practice this means ensuring that the most recently merged pull request was
merged into the `master` branch using the "Merge commit" option.
### 1. Fetch the latest version of the [master branch of the BIDS-specification](https://github.com/bids-standard/bids-specification/tree/master)
You should have a remote, which we will call `upstream`, for the
[bids-standard/bids-specification](https://github.com/bids-standard/bids-specification/)
repository:
show original
We look forward to hearing your feedback!
The BIDS maintainers
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