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[FIX] Do not require notch frequencies to be parsed as numbers, accommodating multiples #1605

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merged 4 commits into from Sep 21, 2023

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effigies
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@effigies effigies commented Aug 31, 2023

While schematizing, the notch column was defined as a number. In the case of iEEG at least, the BEP leads had submitted examples where notch took the form [F1, F2, F3]. This PR recognizes this as existing practice and suggests that curators and tools adopt [F1, F2, ...] for interoperability, but does not require it.

cc @bids-standard/raw-electrophys for comment.

Closes bids-standard/bids-examples#395.

@effigies effigies added MEG Magnetoencephalography iEEG EEG Electroencephalography schema Issues related to the YAML schema representation of the specification. Patch version release. labels Aug 31, 2023
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codecov bot commented Aug 31, 2023

Codecov Report

Patch and project coverage have no change.

Comparison is base (d56b689) 87.83% compared to head (296cebc) 87.83%.

❗ Current head 296cebc differs from pull request most recent head 4035e76. Consider uploading reports for the commit 4035e76 to get more accurate results

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  Files          16       16           
  Lines        1356     1356           
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  Hits         1191     1191           
  Misses        165      165           

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I left some comments cuz this has been an issue for me in the past. Hopefully it helps!

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@effigies effigies changed the title FIX: Notch frequencies may be specified by three numbers FIX: Do not require notch frequencies to be parsed as numbers, accommodating triplets Sep 8, 2023
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effigies commented Sep 8, 2023

@adam2392 Are you comfortable with the current wording leaving open the possibility of a more structured recommendation/requirement in the future?

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The [low, center, high] is incorrect. The line noise is at 60Hz, so that is where you apply a notch. You sometimes also apply a notch filter to the harmonics at 120 and 180 Hz. Therefore 60Hz should not be referred to as 'low' and 120Hz is definitely not 'center'.

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effigies commented Sep 8, 2023

Thank you for the clarification. Is the current wording better?

@effigies effigies changed the title FIX: Do not require notch frequencies to be parsed as numbers, accommodating triplets FIX: Do not require notch frequencies to be parsed as numbers, accommodating multiples Sep 8, 2023
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Yes, thank you! Just a minor suggestion is to say: "If notch filters are applied at multiple frequencies, these frequencies MAY ..."

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I am aware that this PR is mostly to get an already existing practice finally incorporated into the spec, but it irks me that this is not very in line with:

Do you think we should RECOMMEND specifying the frequencies as a comma separated list like 60, 120, 240, and clarify that an old method of [60, 120, 240] is DEPRECATED?

Either way, I am approving this, because I am fine with my suggestion being dealt with in a separate PR. Thanks everyone.

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@Andesha is this something you'd feel comfortable taking a moment to review?

@rwblair rwblair merged commit d567906 into bids-standard:master Sep 21, 2023
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@effigies effigies deleted the schema/notch-type branch September 21, 2023 20:10
@sappelhoff sappelhoff changed the title FIX: Do not require notch frequencies to be parsed as numbers, accommodating multiples [FIX] Do not require notch frequencies to be parsed as numbers, accommodating multiples Nov 13, 2023
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ieeg_filtered_speech incorrect type for notch column values.
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