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[FIX] Clarify run entity to accommodate multiple imaging modalities #760

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merged 3 commits into from
Apr 6, 2022

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yarikoptic
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As we have now other modalities, such as EEG and MEG, "scan" is not really the
most appropriate term here. Having said that we do use _scans etc for EEG and
MEG as well ATM, as it was the "forward compatible" with existing MRI-centric
BIDS back then.

@effigies
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My intuition would be that a "data sample" is a volume, while "recording" would cover a time series. Not sure how other modalities would think about it.

This isn't an objection, just trying to see if there's a clearer word. I'm okay with "data sample" if it's clear to most people.

@yarikoptic yarikoptic mentioned this pull request Mar 17, 2021
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FWIW, I am not entirely happy with "data sample" either for the reasons you have stated. May be someone could suggest a better name...

@sappelhoff
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I think I would find "recordings" most intuitive. But I don't think "scans" is a problem either - in particular because we do use scans.tsv for (structly speaking) non-scanning modalitites (EEG, ...)

-If several scans with the same acquisition parameters ...
+If several recordings (e.g., MRI scans) with the same acquisition parameters ...

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this is a relatively minor thing, but perhaps some more @bids-standard/maintainers have an opinion so that we can address this?

@sappelhoff sappelhoff added the opinions wanted Please read and offer your opinion on this matter label Nov 29, 2021
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FYI, I rebased on master and force pushed.

@tsalo
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tsalo commented Mar 29, 2022

I agree that recording is a bit clearer than data sample, but the definition of "run" under common principles explicitly links it to "data acquisition". Should we use that instead?

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codecov bot commented Mar 29, 2022

Codecov Report

Merging #760 (8bcaba2) into master (7ec7450) will increase coverage by 0.96%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #760      +/-   ##
==========================================
+ Coverage   70.53%   71.50%   +0.96%     
==========================================
  Files           9        9              
  Lines         930      930              
==========================================
+ Hits          656      665       +9     
+ Misses        274      265       -9     
Impacted Files Coverage Δ
tools/schemacode/schemacode/tests/test_schema.py 100.00% <0.00%> (ø)
tools/schemacode/schemacode/_version.py 38.90% <0.00%> (+2.59%) ⬆️

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@sappelhoff sappelhoff merged commit e140f35 into bids-standard:master Apr 6, 2022
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fyi @yarikoptic we discussed this in yesterday's maintainers meeting and as all suggestions to date were improvements, we just decided to just go with one of them.

@sappelhoff sappelhoff changed the title [FIX] run entity - "scans" -> "data samples" [FIX] run entity - "scans" -> "data acquisitions" Apr 6, 2022
@sappelhoff sappelhoff removed the opinions wanted Please read and offer your opinion on this matter label Jul 27, 2022
@effigies effigies changed the title [FIX] run entity - "scans" -> "data acquisitions" [FIX] Clarify run entity to accommodate multiple imaging modalities Jul 27, 2022
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4 participants