FAQ

Cogitate M-EEG BIDS FAQs

Where are the trans files?

The trans.fif files are provided under /derivatives/coreg. They are the results of the coregistration. This information is also included as landmarks in sidecar json of the NIFTI file.

What is under derivatives/additional_metadata?

This directory contains some additional metadata collected along with the data. The top level METADATA directory contains some files common to all subjects: They are analysis.json, devices_MEEG.json, protocols.json, tasks_EXP1_MEEG.json, tasks_RestinEO_MEEG.json, tasks_Rnoise_MEEG.json, wiring_MEEG.pdf.

Subject level directories contain three files: CXXXX_CRF.json, CXXXX_demographics.json, CXXXX_EXQU.json which are respectively subject specific demographics, case report form and the exit questionnaire. The demographics information is redundant with the information in the participants.tsv files.

What does BATCH1 mean?

The M-EEG datasets for COGITATE are being released in two batches in order to facilitate the BIOMAG Connectivity Challenge 2024. This means that one half of the data is initially made available to the participants of the challenge followed by the second half a few months later. This is where BATCH1 and BATCH2 come in.

I cannot find the EOG channel in the data?

The EOG channel for site A can be found in EOG004 and the EOG channels for site B can be found in BIO002. Typically in our code, we prefer to rename the channels as below.

# Fix EOG001 channel name (required for CA only)
if 'EOG004' in raw.ch_names:
raw. rename_channels ({ 'EOG004': 'EOG001'})

# Fix EOG001 channel name(required for CB only)
eog_ch = raw.copy().pick_types(meg=False, eeg=False, eog=True)
if len(eog_ch. ch_names) < 2:
raw.set_channel_types({'BIO002': 'eog'})
raw.rename_channels({'BIO002': 'EOG002'})

What do the channels MISC1, MISC2 and MISC3 contain?

These channels contain the eye tracker data with MISC1 (X), MISC2 (Y), and MISC3 (pupil) channels containing the X, Y (gaze) and the Pupil information respectively. This information is however also shared separately in the eye tracking data release.

Cogitate iEEG BIDS FAQs

What are the coordinates describing the electrodes in electrodes.tsv files?

The electrodes.tsv files contain the coordinates in MNI space.

What do the label files contain?

The label files contain the labels that match the electrode location for the “desikan” or “destrieux” atlas obtained using the mne.get_montage_volume_labels with the electrodes coordinates in subject native T1 space.

How can we get started with using and understanding the IEEG data?

The data may be best understood using the example pipelines provided via Jupyter notebooks at this repository - https://github.com/Cogitate-consortium/iEEG-data-release.

What does the “derivatives/additional_metadata” directory contain?

The additional_metadata directories contain the Case Report forms and Exit Questionnaire information obtained during measurement time. These files are made available for the individual subjects in JSON format. The directory also contains various GENEMEDE style files describing the protocols, analysis, devices and wiring diagrams used during the IEEG data collection.