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| ''' You are free to use all data in OMEGA for research purposes; however, we ask that you please cite the following reference in your publications if you have used data from OMEGA: ''' | ''' '''You are free to use all data in OMEGA for research purposes; however, we ask that you '''please cite the following reference''' in your publications if you have used data from OMEGA: |
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| ''Niso G, Rogers C, Moreau JT, Chen LY, Madjar C, Das S, Bock E, Tadel F, Evans A, Jolicoeur P, Baillet S. OMEGA: The Open MEG Archive. Neuroimage. 2015; Available from: http://dx.doi.org/10.1016/j.neuroimage.2015.04.028'''''''' | Niso G, Rogers C, Moreau JT, Chen LY, Madjar C, Das S, Bock E, Tadel F, Evans A, Jolicoeur P, Baillet S<<BR>>[[http://dx.doi.org/10.1016/j.neuroimage.2015.04.028|OMEGA: The Open MEG Archive]], Neuroimage, 2015. |
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| * The anatomical fiducials (NAS, LPA, RPA) have already been marked and saved in the files fiducials.m | |
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| First, make sure you have enough space on your hard drive, at least '''350Gb''': | * First, make sure you have at least '''20Gb''' of free space on your hard drive (raw files: 12Gb). * The OMEGA database is not in it its final release stage, so we temporarily distribute the 5 subjects used in this tutorial from the Brainstorm website. * Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page, and download the file: '''sample_omega.zip ''' |
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| * Raw files: '''100Gb''' * Processed files: '''250Gb''' * |
* Unzip it in a folder that is not in any of the Brainstorm folders (program folder or database folder). |
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| * Start Brainstorm (Matlab scripts or stand-alone version). For help, see the [[http://neuroimage.usc.edu/brainstorm/Installation|Installation]] page. | |
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| * Select the menu File > Create new protocol. Name it "'''TutorialOmega'''" and select the options: * "'''No, use individual anatomy'''", * "'''No, use one channel file per condition'''". == Import the dataset == * The datasets organized following the [[http://bids.neuroimaging.io|BIDS specifications]] can be imported semi-automatically. * Select the menu File > Load protocol > '''Import BIDS dataset''' > Select the folder '''sample_omega'''. * Keep the default values for all the questions that may be asked during the import process (eg. number of vertices in the cortex surfaces). Once finished, you should be able to see 5 subjects in your database explorer: anatomy, and subject and noise recordings. <<BR>><<BR>> * The files that have been imported with this process are the following: * sample_omega/derivatives/freesurfer/sub-000*_ses-0001: MRIs processed with FreeSurfer. * sample_omega/sub-000*/ses-0001/meg/*_task-rest_run-01_meg.ds: Resting MEG recordings * sample_omega/sub-000*/ses-0001/meg/*_task-noise_run-01_meg: Empty room recordings |
Resting state recordings from the OMEGA database
Authors: Francois Tadel, Guiomar Niso, Elizabeth Bock.
This tutorials introduces how to download a resting state recordings from the OMEGA database, and how to process them into Brainstorm.
License
The Open MEG Archive (OMEGA) is the fruit of a collaborative effort by the McConnell Brain Imaging Centre and the Université de Montréal to build a centralised repository in which to regroup MEG data for open dissemination. This continuously expanding repository also contains anatomical MRI volumes, demographic and questionnaire information, and eventually will feature other forms of electrophysiological data (e.g. EEG, field, and cell recordings). OMEGA features the technological framework for multi-centric data aggregation, and is amongst the largest freely available resting-state MEG datasets presently available.
You are free to use all data in OMEGA for research purposes; however, we ask that you please cite the following reference in your publications if you have used data from OMEGA:
Niso G, Rogers C, Moreau JT, Chen LY, Madjar C, Das S, Bock E, Tadel F, Evans A, Jolicoeur P, Baillet S
OMEGA: The Open MEG Archive, Neuroimage, 2015.
Presentation of the experiment
Experiment
- 5 subjects
- 5 minute resting sessions, eyes open
MEG acquisition
Acquisition at 2400Hz, with a CTF 275 MEG system,
- Recorded at the Montreal Neurological Institute in 2015-2016.
- Anti-aliasing low-pass filter at 600Hz, files saved with the CTF 3rd order gradient compensation.
- Recorded channels (340):
- 1 Stim channel indicating the presentation times of the audio stimuli: UPPT001 (#1)
- 1 Audio signal sent to the subject: UADC001 (#316)
- 1 Response channel recordings the finger taps in response to the deviants: UDIO001 (#2)
- 26 MEG reference sensors (#5-#30)
- 274 MEG axial gradiometers (#31-#304)
- 2 EEG electrodes: Cz, Pz (#305 and #306)
- 1 ECG bipolar (#307)
- 2 EOG bipolar (vertical #308, horizontal #309)
- 12 Head tracking channels: Nasion XYZ, Left XYZ, Right XYZ, Error N/L/R (#317-#328)
- 20 Unused channels (#3, #4, #310-#315, #329-340)
The data in this dataset has been formatted along the BIDS specifications (Brain Imaging Data Structure, http://bids.neuroimaging.io)
Head shape and fiducial points
- 3D digitization using a Polhemus Fastrak device driven by Brainstorm. The .pos files contain:
- The position of the center of CTF coils
The position of the anatomical references we use in Brainstorm: Nasion and connections tragus/helix, as illustrated here
- Around 150 head points distributed on the hard parts of the head (no soft tissues)
Subject anatomy
- Structural T1 image recorded with a 1.5T MRI
Processed with FreeSurfer 5.3
- The anatomical fiducials (NAS, LPA, RPA) have already been marked and saved in the files fiducials.m
Download and installation
First, make sure you have at least 20Gb of free space on your hard drive (raw files: 12Gb).
- The OMEGA database is not in it its final release stage, so we temporarily distribute the 5 subjects used in this tutorial from the Brainstorm website.
Go to the Download page, and download the file: sample_omega.zip
- Unzip it in a folder that is not in any of the Brainstorm folders (program folder or database folder).
Start Brainstorm (Matlab scripts or stand-alone version). For help, see the Installation page.
Select the menu File > Create new protocol. Name it "TutorialOmega" and select the options:
"No, use individual anatomy",
"No, use one channel file per condition".
Import the dataset
The datasets organized following the BIDS specifications can be imported semi-automatically.
Select the menu File > Load protocol > Import BIDS dataset > Select the folder sample_omega.
Keep the default values for all the questions that may be asked during the import process (eg. number of vertices in the cortex surfaces). Once finished, you should be able to see 5 subjects in your database explorer: anatomy, and subject and noise recordings.
- The files that have been imported with this process are the following:
sample_omega/derivatives/freesurfer/sub-000*_ses-0001: MRIs processed with FreeSurfer.
- sample_omega/sub-000*/ses-0001/meg/*_task-rest_run-01_meg.ds: Resting MEG recordings
- sample_omega/sub-000*/ses-0001/meg/*_task-noise_run-01_meg: Empty room recordings