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[FIX] document required column order MEG, EEG, iEEG, PET, and fix typo iEEG #818

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merged 2 commits into from
Jun 11, 2021

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sappelhoff
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closes #817

The EEG and iEEG specs had sentences like "columns X, Y, ... are required" before the table outlining the requirement levels. For the iEEG spec, this was furthermore inconsistent.

I removed these sentences before the tables as duplicate information, thereby also fixing the ieeg inconsistency.

I furthermore added a note to the tables where the order column is mandatory. This was not documented consistently before, and many people probably only found out about this by getting the validator error that is generated by these lines:

https://github.com/bids-standard/bids-validator/blob/c60daacf3dbb4cea5a07d5274947c366cf4c0e3a/bids-validator/validators/tsv/tsv.js#L243-L298

@dorahermes I saw your comment voting for making the column order of ieeg files consistent with those of EEG and MEG (only name, type, units, instead of additionally low and high cutoff). But that'd be a more invasive change that I don't think is necessary at this point (no complaints or issues have been raised about this). Let me know if you think otherwise.

@sappelhoff sappelhoff requested review from dorahermes and Remi-Gau June 6, 2021 08:23
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Thank you! lgtm

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@sappelhoff sounds good to leave difference between iEEG/EEG&MEG for now, this already makes things much clearer.

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Remi-Gau commented Jun 9, 2021

Thanks for implementing this @sappelhoff

Had no idea some TSV even have required column orders: any other tables with that required fetaure?

@sappelhoff
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Had no idea some TSV even have required column orders: any other tables with that required fetaure?

yes 🤔 good point, blood.tsv wants "time" in the first column:

https://github.com/bids-standard/bids-validator/blob/c60daacf3dbb4cea5a07d5274947c366cf4c0e3a/bids-validator/validators/tsv/tsv.js#L300-L307

But it's not described in the spec as far as I can see?

https://github.com/bids-standard/bids-specification/blame/master/src/04-modality-specific-files/09-positron-emission-tomography.md#L335-L339

cc @mnoergaard @melanieganz

Did I oversee a note that time MUST be the first column in blood.tsv? Or is it not there?

If it's not there, do we want to:

  1. add a note to the spec?
  2. or remove this requirement from the validator?

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Yes - when implementing the validator we wanted to have "time" as the first column to impose a certain structure. I would suggest to add a note to the spec on this when introducing the columns for the blood data. It could be something like this:

"The following columns are defined for _blood.tsv files, and the time column should always be positioned in the first column: "

@sappelhoff sappelhoff changed the title [FIX] inconsistency in ieeg table and text, document required column order MEG, EEG, iEEG [FIX] document required column order MEG, EEG, iEEG, PET, and fix typo iEEG Jun 10, 2021
@sappelhoff sappelhoff force-pushed the fix/ieeg/table_vs_text branch from bd100a3 to c1c3d89 Compare June 10, 2021 10:43
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Thanks @mnoergaard , I added a note. Please add an approving review if you think this is fine.

@sappelhoff sappelhoff requested a review from mnoergaard June 10, 2021 10:44
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LGTM, thanks @sappelhoff!

@sappelhoff sappelhoff merged commit 709299d into bids-standard:master Jun 11, 2021
@sappelhoff sappelhoff deleted the fix/ieeg/table_vs_text branch June 11, 2021 07:11
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inconsistencies between text and table for channels.tsv for iEEG
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