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[WIP] Eyetrack-EEG dataset #389

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Remi-Gau
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@Remi-Gau Remi-Gau commented Jul 6, 2023

for BEP20

from @arnodelorme suggestion

see here
bids-standard/bids-specification#1128 (comment)

TODO

  • merge events files from eyetrack and eeg
  • add missing required metadata
  • update eyetrack.json to document what other columns are
  • update dataset listing

@arnodelorme
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Thanks @Remi-Gau I assume all the checks need to pass (is that running the BIDS validator?).

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Remi-Gau commented Jul 6, 2023

Thanks @Remi-Gau I assume all the checks need to pass (is that running the BIDS validator?).

Don't worry about the checks for now because they will only ever pass once the validator has been updated to validate eyetracking data: so failure is expected for now.

@Remi-Gau Remi-Gau marked this pull request as draft July 10, 2023 18:52
@arnodelorme
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Do you have an example we could follow? I have looked at all of the ones listed on mszinte/bids-specification#3

However, none contains EEG and eye-tracking data (or even eye-tracking as a secondary measure). I am happy to move files around, but I am also unclear on what you mean by "add missing required metadata" and "update dataset listing"

If there is no example and no existing documentation, I will do what I can and you can provide feedback. Thanks

@Remi-Gau
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Do you have an example we could follow? I have looked at all of the ones listed on mszinte/bids-specification#3

No example or precedent I am afraid. We are making history: the thrill of working on BEP... Sigh...

However, none contains EEG and eye-tracking data (or even eye-tracking as a secondary measure). I am happy to move files around

but I am also unclear on what you mean by "add missing required metadata"

Will flag the TODOs in comments in the PR

and "update dataset listing"

We need to update this file (not urgent for now)

https://github.com/bids-standard/bids-examples/blob/master/dataset_listing.tsv

If there is no example and no existing documentation, I will do what I can and you can provide feedback. Thanks

@@ -77,3 +77,4 @@ ieeg_visual_multimodal [@irisgroen](https://github.com/irisgroen) anat, fmap,
genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info [@cpernet](https://github.com/cpernet) anat, dwi, fmap, func FLAIR, T1w, bold, dwi, events, info, magnitude1, phasediff
motion_dualtask older and younger participants walking while performing discrimination task [@sjeung](https://github.com/sjeung) eeg, motion channels, eeg, events, motion, scans
motion_spotrotation participants rotated heading using full-body motion or joystick [link](https://openneuro.org/datasets/ds004460) [@sjeung](https://github.com/sjeung) eeg, motion channels, coordsystem, eeg, electrodes, events, motion, scans
eyetrack_eeg eye-tracking (plus simultaneous EEG) dataset https://drive.google.com/drive/folders/1kzI5Lwg__BvDKGup37QO2lLLzBTlHe0L?usp=sharing [@arnodelorme](https://github.com/arnodelorme) eeg channels, coordsystem, eeg, electrodes, events, eyetrack
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@arnodelorme not sure if the dataset will be on google drive forever

if the actual data is stored somewhere in the end, the link in the tsv will have to be updated

Comment on lines +4 to +6
"ScreenDistance": "REQUIRED",
"ScreenResolution": "REQUIRED",
"ScreenSize": "REQUIRED"
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REQUIRED metadata missing

Comment on lines +3 to +4
"SampleCoordinateUnit": "REQUIRED",
"SampleCoordinateSystem": "REQUIRED",
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REQUIRED metadata missing

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not checked this file but it may be good to truncate it at least partially to avoid getting bloating the repo

also this tsv has a lot of extra columns: this is fine but it would be a better examples if their content was described in its side car json

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Thanks @Remi-Gau
@deepagupta please use the files in https://drive.google.com/drive/folders/1kzI5Lwg__BvDKGup37QO2lLLzBTlHe0L?usp=drive_link
And modify them according to Remi's advises on this tread. We can check them together before showing them to Remi

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@Remi-Gau , one more question. The eye-tracking and EEG are at different sampling rates, yet they will share the same event file. I assume this means that the eye-tracking data need to be upsampled x10. This is far from ideal (and a lot of people will complain about that). Any other suggestions?

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@Remi-Gau , one more question. The eye-tracking and EEG are at different sampling rates, yet they will share the same event file. I assume this means that the eye-tracking data need to be upsampled x10. This is far from ideal (and a lot of people will complain about that). Any other suggestions?

Silly suggestion: I think that then the value and sample columns would then have to be dropped: those columns are be moved from optional to arbitrary.
See: bids-standard/bids-specification#1457

I am sure that there are potential issues I am missing with this approach so let me know what you think.

Comment on lines +5 to +9
0.074626866 226 10 93 0
1.76119403 46 236 4 1
2.104477612 348 282 8 1
4.701492537 76 630 4 1
5.268656716 433 706 8 1
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@arnodelorme
are those durations in seconds?

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yes, first column is in second. The second column is in samples for the EEG (EEG files) and samples for eye-tracking (eye-tracking file) - but at different sampling rates.

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duration column MUST be in seconds

https://bids-specification.readthedocs.io/en/latest/glossary.html#objects.columns.duration

samples will have to be dropped from the events.tsv if we are merging data with different sampling scheme: this was the old recommendation in the spec before the samples column got dropped altogether from the spec

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OK, I understand about dropping the "sample" column.

@Remi-Gau Remi-Gau mentioned this pull request Nov 28, 2023
40 tasks
@arnodelorme
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Following your advice @Remi-Gau, I have finally worked out the alignment of EEG and eye-tracking using both the SMI and the Gazepoint eyetrackers. The BIDS repo passes the validator except for the eye-tracking files.

The export (including data) is available at https://drive.google.com/drive/folders/1jEKySJdLc2cdO12y_MENxUHC95cjVIq9?usp=sharing

@Remi-Gau Remi-Gau added the BEP label Aug 27, 2024
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