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[FIX] add paragraph on MEG specific "markers" suffix in MEG spec#653

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[FIX] add paragraph on MEG specific "markers" suffix in MEG spec#653
sappelhoff merged 5 commits intobids-standard:masterfrom
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@sappelhoff sappelhoff commented Oct 25, 2020 •
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closes #638 --> the *_markers suffix was only defined in the appendix and occurred quite unexpectedly and randomly.

If we could turn back time we would probably solve the issue on "how to define KIT marker files" without adding a new suffix entirely for that issue.

I suggest this minor fix (this PR) to at least increase transparency of the "markers" suffix in the spec text.

For future enhancements it'd be cool if we could think of a way to somehow salvage the "markers" suffix in a backwards compatible way and put it to some use beyond KIT/Yokogawa/Ricoh. --> suggestions in that direction are very welcome.

The relevant part of the diff is this sentence (rest is typos, linebreaks, a link fix. and a historical perspective in the appendix):

+
+Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh sytem,
+which saves the MEG sensor coil positions in two separate files (`.sqd`, `.mrk`).
+For these files, the `markers` suffix MUST be used.
+For example: `sub-01_task-nback_markers.sqd`
+
Please refer to [Appendix VI](../99-appendices/06-meg-file-formats.md)
for general information on how to deal with such manufacturer specifics and to see more examples.

tsalo
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Overall looks good.

teonbrooks
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Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
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hoechenberger commented Oct 27, 2020

Super late to the party, but why can we not name those marker files *_meg.sqd and *_meg.mrk, so we wouldn't need the markers suffix?

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sappelhoff commented Oct 27, 2020

Super late to the party, but why can we not name those marker files *_meg.sqd and *_meg.mrk, so we wouldn't need the markers suffix?

that would make sense to me, would be good to go that way.

We'd then still have to document and deprecate the markers suffix

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teonbrooks commented Oct 27, 2020

*_meg.sqd

this is the same name as the raw file so it would likely collide naming-wise

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hoechenberger commented Oct 27, 2020

this is the same name as the raw file so it would likely collide naming-wise

Oh, darn, I wasn't aware of this! Ok, in that case we cannot do this. Sorry about the confusion.

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teonbrooks commented Oct 27, 2020

it is a historical and inconsistent pattern that was introduced. here's a brief history from what I can recall:

the original extension for Ricoh continuous data was .sqd. This was later modernized to .con (to denote continuous I believe) but to preserve backwards compatibility .sqd is still valid and acceptable for the raw, continuous data file.

the original extension for Ricoh marker file was .sqd as well. To determine if it is continuous data or marker file, the internal header file specified this. This was later modernized to .mrk to disambiguate files but to preserve backwards compatibility, .sqd is acceptable.

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Update src/04-modality-specific-files/02-magnetoencephalography.md
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#653 (comment)

Co-authored-by: Teon L Brooks <teon.brooks@gmail.com>
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sappelhoff commented Oct 27, 2020

awesome, thanks for shedding some light on this @teonbrooks!

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add historical perspective on KIT/yokogawa/ricoh data
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Co-authored-by: Teon L Brooks <teon.brooks@gmail.com>
@sappelhoff sappelhoff requested a review from tsalo October 28, 2020 09:08
@sappelhoff sappelhoff merged commit 8209147 into bids-standard:master Oct 30, 2020
@sappelhoff sappelhoff deleted the markers branch October 30, 2020 09:40
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[DOC] Auto-generate changelog entry for PR #653
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markers suffix for MEG only referenced in Appendix VI

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