[WIP] Eyetrack-EEG dataset #389

Remi-Gau · 2023-07-06T09:04:03Z

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 · 2023-07-06T09:26:38Z

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

Remi-Gau · 2023-07-06T09:29:42Z

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.

arnodelorme · 2023-07-10T19:43:55Z

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

eyetrack_eeg/sub-001/eeg/sub-001_task-HBNdata_eyetrack.json

Remi-Gau · 2023-07-10T19:51:33Z

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

Remi-Gau · 2023-07-10T19:53:12Z

dataset_listing.tsv

@@ -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


@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

Remi-Gau · 2023-07-10T19:54:05Z

eyetrack_eeg/sub-001/eeg/sub-001_task-HBNdata_events.json

+      "ScreenDistance": "REQUIRED",
+      "ScreenResolution": "REQUIRED",
+      "ScreenSize": "REQUIRED"


REQUIRED metadata missing

Remi-Gau · 2023-07-10T19:54:19Z

eyetrack_eeg/sub-001/eeg/sub-001_task-HBNdata_eyetrack.json

+  "SampleCoordinateUnit": "REQUIRED",
+  "SampleCoordinateSystem": "REQUIRED",


REQUIRED metadata missing

Remi-Gau · 2023-07-10T19:56:22Z

eyetrack_eeg/sub-001/eeg/sub-001_task-HBNdata_eyetrack.tsv

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

arnodelorme · 2023-07-10T20:56:23Z

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

arnodelorme · 2023-07-10T20:59:23Z

@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?

Remi-Gau · 2023-07-10T21:31:38Z

@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.

Remi-Gau · 2023-07-10T21:32:44Z

eyetrack_eeg/sub-001/eye/sub-001_task-HBNdata_events.tsv

+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


@arnodelorme
are those durations in seconds?

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.

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

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

arnodelorme · 2024-02-02T22:28:56Z

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 added 3 commits July 5, 2023 13:31

add eyetrack dataset

2af8495

rename

39b8902

rename

d8e8f1a

Remi-Gau mentioned this pull request Jul 6, 2023

[ENH] BEP 020 Eye Tracking bids-standard/bids-specification#1128

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9 tasks

add metadata

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update listing

ba60854

Remi-Gau marked this pull request as draft July 10, 2023 18:52

Remi-Gau commented Jul 10, 2023

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Remi-Gau commented Jul 10, 2023

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[WIP] Eyetrack-EEG dataset #389

[WIP] Eyetrack-EEG dataset #389

Remi-Gau commented Jul 6, 2023 •

edited

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arnodelorme commented Jul 10, 2023

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arnodelorme commented Feb 2, 2024

		"SampleCoordinateUnit": "REQUIRED",
		"SampleCoordinateSystem": "REQUIRED",

[WIP] Eyetrack-EEG dataset #389

Are you sure you want to change the base?

[WIP] Eyetrack-EEG dataset #389

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Remi-Gau commented Jul 6, 2023 • edited

TODO

arnodelorme commented Jul 6, 2023

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arnodelorme commented Feb 2, 2024

Remi-Gau commented Jul 6, 2023 •

edited