[ENH] Propose to use *_channels.json for the description of coordinate systems

[JuliusWelzel]

Hello,

as discussed before, we would like to move the description of coordinate system information for motion data from the *_motion.json to the *_channels.json file.

@sjeung already implemented this in her example datasets, I will not get around to do this before my holiday :(
We updated the schema accordingly.

Please check if the PR seems ok.

Best,
Julius

[sappelhoff]

we also need to remove the references to RotationRule, RotationOrder, and SpatialAxes here:

bids-specification/src/schema/rules/sidecars/motion.yaml

Lines 74 to 75 in 8c9fa11

	RotationOrder: recommended
	RotationRule: recommended

Else they'll keep showing up as recommended fields in motion.json.

Instead we need to add some schema magic to make them show up under channels.json IF the modality is motion. cc @tsalo @effigies

---

furthermore, I think the reference_frame column for channels.tsv should also be mentioned here:

bids-specification/src/modality-specific-files/motion.md

Lines 140 to 144 in 8c9fa11

	This file is REQUIRED as it makes it easy to browse or query over larger collections of datasets.
	The REQUIRED columns are channel `name`, `component`, `type`, `tracked_point` and `units`.
	Any number of additional columns MAY be added to provide additional information about the channels.
	The `*_tracksys-<label>_channels.tsv` file SHOULD give additional information about individual recorded channel,
	some of which my not be found summarized in `*_motion.json`.

and link to the new section that you are introducing ("reference frame description")

[sappelhoff]

would be nice to have a short TSV example with "reference_frame" "local" somewhere. Either a new one here or in the existing example above.

[JuliusWelzel]

I only did one example for now. In my experience that is less complicated, than providing multiple ones. It is mentioned in the text, that the reference_frame column is only RECOMMENDED.

[codecov]

Codecov Report

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[JuliusWelzel]

I implemented @sappelhoff comments in the previous commits. @sjeung can you please check if my suggestion for introducing the reference_frame column is sufficient for now?

[sjeung]

Hi! Both the example and the description in the specification look good from my side.

@JuliusWelzel could you remind me if your example data set is up-to-date?
My updated examples can be found here .

For validator I only removed the fields from motion.json.
@tsalo @effigies @sappelhoff, Do you have any suggestions on whether to validate the channels.json according to this part of the spec?

[effigies]

Started to comment here, just made edits instead: #1591

Diff from this PR: https://github.com/JuliusWelzel/bids-specification/compare/master...effigies:bids-specification:channels-json

[effigies]

Do you have any suggestions on whether to validate the channels.json according to this part of the spec?

I don't know how to validate that in the legacy validator. In the schema validator, you can't currently validate anything inside column descriptions. I'm not sure what the best path forward for that would be. (Flagging @rwblair, as we'll need to think about this.)

[JuliusWelzel]

@sappelhoff This PR should be merged into main before the release as it clarifies how to describe coordinate systems for motion data. Is there anything we can do to help speed up the process?

[effigies]

@JuliusWelzel Could you review #1591? It contains these proposals:

c00d1c1...6ab3e00

[JuliusWelzel]

@JuliusWelzel Could you review #1591? It contains these proposals:

c00d1c1...6ab3e00

Looks good to me. Will will update the Examples accordingly. Thanks!

[JuliusWelzel]

Will will update the Examples accordingly.

Examples have been updated here, I think it is ready to be merged.

Minor changes to specs have been made as well

[sappelhoff]

• closing as replaced by [ENH] Add Level objects to channels.json for motion #1591