Tutorial 4: Channel file and coregistration MEG-MRI

Authors: Francois Tadel, Elizabeth Bock, Sylvain Baillet

The anatomy of your subject is ready. Before we can start looking at the MEG/EEG recordings, we need to make sure that the sensors (electrodes, magnetometers or gradiometers) are properly aligned with the MRI and the surfaces of the subject.

In this tutorial, we will start with a detailed description of the experiment and the files that were recorded, then we will link the original CTF files to the database in order to get access to the sensors positions, and finally we will explore the various options for aligning these sensors on the head of the subject.

Auditory dataset

This dataset used in the introduction tutorials is the same as the one used in the MEG Auditory tutorial:


This tutorial dataset (MEG and MRI data) remains a property of the MEG Lab, McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Canada. Its use and transfer outside the Brainstorm tutorial, e.g. for research purposes, is prohibited without written consent from the MEG Lab.

If you reference this dataset in your publications, please aknowledge its authors (Elizabeth Bock, Peter Donhauser, Francois Tadel and Sylvain Baillet) and cite Brainstorm as indicated on the website. For questions, please contact us through the forum.

Presentation of the experiment


  • One subject, two acquisition runs of 6 minutes each
  • Subject stimulated binaurally with intra-aural earphones (air tubes+transducers)
  • Each run contains:
    • 200 regular beeps (440Hz)
    • 40 easy deviant beeps (554.4Hz, 4 semitones higher)
  • Random inter-stimulus interval: between 0.7s and 1.7s seconds, uniformly distributed
  • The subject presses a button when detecting a deviant with the right index finger
  • Auditory stimuli generated with the Matlab Psychophysics toolbox
  • The specifications of this dataset were discussed initially on the FieldTrip bug tracker:

MEG acquisition

  • Acquisition at 2400Hz, with a CTF 275 system, subject in sitting position

  • Recorded at the Montreal Neurological Institute in December 2013
  • Anti-aliasing low-pass filter at 600Hz, files saved with the 3rd order gradient
  • 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)
  • 3 datasets:
    • S01_AEF_20131218_01.ds: Run #1, 360s, 200 standard + 40 deviants

    • S01_AEF_20131218_02.ds: Run #2, 360s, 200 standard + 40 deviants

    • S01_Noise_20131218_01.ds: Empty room recordings, 30s long

    • File name: S01=Subject01, AEF=Auditory evoked field, 20131218=date(Dec 18 2013), 01=run
  • Average reaction times for the button press after a deviant tone:
    • Run #1: 515ms +/- 108ms

    • Run #2: 596ms +/- 134ms

  • Use of the .ds, not the AUX (standard at the MNI) because they are easier to manipulate in FieldTrip

Head shape and fiducial points

  • 3D digitization using a Polhemus Fastrak device driven by Brainstorm (S01_20131218_*.pos)

  • More information: Digitize EEG electrodes and head shape

  • The output file is copied to each .ds folder and contains the following entries:
    • 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)

Automatic registration

The registration between the MRI and the MEG (or EEG) is done in two steps. We start with a first approximation based on three reference points, then we refine it with the full head shape of the subject.

Step 1: Fiducials

Step 2: Head shape

New files and folders

Many new files are now visible in the database explorer:

Each of those new folders show two elements:

Review vs Import

When trying to bring external data into the Brainstorm environment, a common source of confusion is the difference between the two popup menus Review and Import:

Display the sensors

Right-click on the CTF channels file and try all the display menus:


Manual registration

If the registration you get with automatic alignment techniques described previously, or if there was an issue when you digitized the position of the fiducials or the head shape, you may have to realign manually the sensors on the head. Right-click on the channel file > MRI Registration:

There is nothing to change here, but remember to always check the registration scalp/sensors.

Multiple runs and head positions

Between two acquisition runs the subject may move in the MEG helmet, the relative position of the MEG sensors with the head surface changes. At the beginning of each MEG run, the positions of the head localization coils are detected and used to update the position of the MEG sensors.

Edit the channel file

Display a table with all the information about the individual channels. You can edit all the values.


What's in the channel file

Some other fields are present in the channel file that cannot be accessed with the Channel editor window. You can explore those other fields with the File menu, selecting View file contents or Export to Matlab, as presented in the previous tutorial.

Some fields you may find there:

Feedback: Comments, bug reports, suggestions, questions
Email address (if you expect an answer):

Tutorials/ChannelFile (last edited 2015-06-30 20:29:19 by FrancoisTadel)