Data Hosting & Sharing: The Open MEG Archive (OMEGA)

OMEGA logo
Welcome to the Open MEG Archive (OMEGA)

The Open MEG Archive (OMEGA) is the fruit of a collaboration between the McConnell Brain Imaging Centre (BIC) of the Montreal Neurological Institute-Hospital at McGill University, and the Université de Montréal, with the purpose of providing a core repository of MEG data for open science.

Purpose

OMEGA is amongst the largest repository of MEG data presently available. It is a continuously expanding resource that also contains anatomical MRI volumes, demographic and questionnaire information. OMEGA may also feature multimodal electrophysiological data (e.g., EEG, field and cell recordings).

The primary objective of OMEGA is the conservation of brain imaging data collected with different brain imaging techniques and behavioral tests scores from healthy and patient volunteers (any age range), in order to allow future research in the field of high-powered detection of effects of interest in human brain activity.

OMEGA in a resource to establish typical features of brain activity, in relation to demographic factors (age, gender, standardized behavioral tests scores, etc.) and to reveal new markers of abnormal brain activity in various pathologies.

We hope OMEGA contributes to open scientific research, for the advancement of knowledge, and the greater good.


Highlights

  • First open data repository fully dedicated to MEG.
  • MEG data from 294 new* participants (*see next section): 161 healthy controls and 134 patient volunteers (127 Parkinson, 7 chronic pain). About 900 resting-state MEG recordings totalling over 75 hours of data.
  • Now structured according to the Brain Imaging Data Structure (v1.7.0).
  • Directly readable by data-analysis software like Brainstorm.
  • Anatomical T1-weighted MRI volumes (defaced) of most participants.
  • Demographic and standardized questionnaire data.

Participants

Group Sex 20 - 30 - 40 - 50 - 60 - 70 - 80+ Tot
Control F 4 3 2 11 75 25 1 121
  M 3   1 2 23 9 2 40
Parkinson F     2 14 9 9 3 37
  M     4 20 41 21 3 90
Chronic Pain F           1   1
  M     2 3 1     6
Total   7 3 11 50 149 65 9 294

Current version

The present version is Release 3.0.0: it includes new participants that were not available from previous OMEGA releases. As we are updating data access procedures, we will be re-releasing the data volumes from the previous 220 participants and more in the next upcoming versions of OMEGA - please stay tuned!

Planned future releases:

  • Will include OMEGA data volumes from the original release, with a larger proportion of younger adults.
  • Entirely new data volumes.
  • More detailed co-registration information between MEG and MRI.
  • Data quality checks and reports.

Access

OMEGA promotes open-science good practices via, presently, a controlled access procedure.

You will need to provide your full name, affiliation, and a valid institutional email address (Gmail, Yahoo, iCloud, etc. addresses are not permitted). This information is for verification and curation purposes only, and will not be used outside of OMEGA.

You are also asked to review and accept the following terms of the OMEGA Data Use Agreement:

  • You must agree to respect the data privacy standards in effect in Quebec and Canada. In particular, you must not attempt re-identification of participants nor redistribute the data. Please redirect any request to access your copy of OMEGA to the present page.
  • You must acknowledge that the proposed study has been reviewed and approved by the duly constituted research ethics board(s) that has/have jurisdiction over it – typically the IRB/REB from your home institution. However, if the project originates from a jurisdiction where ethics approval is not required, you must seek and have obtained approval from the MUHC Neurosciences-Psychiatry REB, and provide the approved REB study number at the time of your registration to OMEGA.
  • You will need to keep the retrieved OMEGA data in a secure environment. You shall not share this copy or use it to create a new bank or repository.
  • You will recognize the contribution of OMEGA in all your publications and presentations of study work or results obtained using data from OMEGA.

 

Please click here to register. 

Data

Retrieving data

The data is stored on a secure ownCloud instance at the BIC. ownCloud is an open-source web-based file hosting application similar to Dropbox or Google Drive. Once you have been granted access, you will receive access credentials by email. You can then download files via the following options. Additional configuration details are available on the BIC forum.

  1. Web interface is simple, but not the most efficient for downloading large volumes of data at once.
  2. WebDAV protocol is more complex to set up, depending on the OS, but is a versatile option. It allows mounting the shared directory and copying files with common file managers (e.g., Windows Explorer, Mac OS X Finder, Linux KDE Dolphin) or from the command line. You may try a WebDAV client (e.g., Cyberduck or Rclone) to help with the setup and provide a user-friendly interface to retrieve files. 
  3. ownCloud Desktop Sync client is designed to synchronize files between a local computer and an ownCloud server. It can be used by guests to download shared files.

Data organization

OMEGA is structured according to BIDS 1.7.0.

Apart from some general files in the root folder (dataset_description.json, participants.tsv, CHANGES, LICENSE, etc.), and the demographic information in the phenotype subfolder, the imaging data is organized by participant, session and modality, as the following example:

sub-0000/
    ses-01/
        sub-0000_ses-01_scans.tsv
        anat/
            sub-0000_ses-01_T1w.nii.gz
            sub-0000_ses-01_T1w.json
        meg/
            sub-0000_ses-01_task-noise_run-01_meg.ds
            sub-0000_ses-01_task-noise_run-01_meg.json
            sub-0000_ses-01_task-noise_run-01_channels.tsv
            sub-0000_ses-01_task-rest_run-01_meg.ds
            sub-0000_ses-01_task-rest_run-01_meg.json
            sub-0000_ses-01_task-rest_run-01_channels.tsv
            sub-0000_ses-01_task-restaftertask_run-05_meg.ds
            sub-0000_ses-01_task-restaftertask_run-05_meg.json
            sub-0000_ses-01_task-restaftertask_run-05_channels.tsv
            sub-0000_ses-01_coordsystem.json
            sub-0000_ses-01_headshape.pos

In each session folder, a _scans.tsv table lists the MRI scans and MEG recordings available.

MEG data

OMEGA contains data collected as part of many different studies. A few of the larger projects collect additional data such as clinical info, neuropsychological tests, imaging, genetics, etc. that are shared in separate repositories. In these cases, participant IDs in OMEGA match the IDs in the other repositories. This is currently the case for these two projects:

Currently, OMEGA only contains resting-state MEG recordings. Task recordings may be added in future releases. "Baseline" rest recordings are identified by the task label "rest". If a rest recording was collected after the participants performed a task, the label is "restaftertask".

Empty-room "noise" MEG recordings are also available for most MEG volumes and are included in each session folder, next to the participant's recordings.

The data were all performed with the 275-channel 2005 series CTF MEG system at the McConnell Brain Imaging Center.

Raw MEG data files were renamed, de-identified and structured as BIDS with custom MATLAB code, some of which is available in our CtfMegBids GitHub repository (2022-03-07).

When system issues, environmental noise, or participant-specific artefacts (e.g., dental work or makeup) were noted by the individual acquiring the data, this information is saved in the _meg.json file, in the SubjectArtefactDescription field. We will update this information as it is reported by users or identified by improved quality control procedures.

MRI data

One or more T1w MRI images are included for each participant, when possible, for source imaging purposes.

Raw DICOM images were sorted, de-identified and converted to the NIfTI-1 file format and BIDS structure with heudiconv (0.10.0). Images were then de-faced (facial features distorted to further preserve anonymity) with XNAT Tools: Face Masking (12.27.2017).

Co-registration

Since the anatomical images are de-faced, we aim to soon provide co-registration information in the form of matching anatomical fiducial point coordinates in the MRI _T1w.json file and the MEG _coordsystem.json file. We will use the MRI images, digitized head shape and fiducial points, and pictures of MEG head coil placement, as appropriate given the availability and quality of these data for each subject. This means the fiducial point coordinates saved in the MEG json files may not correspond to the digitized coordinates present in the _headshape.pos file.

Scan dates

As an additional anonymization measure, session dates were shifted by a fixed number of days within each participant volume (the shifting procedure sets the first sessions for each participant to 2000-01-01.) Hence, the relative date difference between sessions for each participant remains meaningful. These relative times can also be obtained with the (fractional) age provided in the sessions table (see demographics section below).

OMEGA general questionnaire

The questionnaire administered to participants evolved over time, therefore the available data varies between subjects. General information such as age, gender, sex, handedness, etc. is available for the bast majority of participants. All questionnaire versions are now combined in a single table.

Some responses from previous versions were recorded in French and still appear as such in the table. We aim to translate most answers in an upcoming release.

The questionnaire is primarily a collection of brief standardized tests. It is described in detail in the file phenotype/OmegaQuestionnaireDescription.pdf, and the questions themselves are provided in the accompanying json files (English and French).

Participant demographics

Basic participant information is provided in the file participants.tsv. As some volunteers participated in multiple studies and their age or category may change between sessions, an additional table is provided with per-session values: phenotype/sessions.tsv. The age and category in the participants table correspond to the first MEG session for each participant.

 

References

Support OMEGA by citing the following article when you publish findings based on data retrieved from OMEGA. 

G. Niso, C. Rogers, J.T. Moreau, L-Y. Chen, C. Madjar, S. Das, E. Bock, F. Tadel, A.C. Evans, P. Jolicoeur, S. Baillet, OMEGA: The Open MEG Archive, NeuroImage, 124B(1) Jan 2016, pp 1182-1187, ISSN 1053-8119. http://dx.doi.org/10.1016/j.neuroimage.2015.04.028

Contact

For any inquiry, please contact Sylvain Baillet, OMEGA Principal Investigator, at sylvain.baillet [at] mcgill.ca (ORCID)

 

                           

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