Tutorial 4: Co-registration MEG-MRI

Authors: Francois Tadel, Elizabeth Bock, Sylvain Baillet

From continuous

Access the raw file

The basic tutorials you read before explain how to import recordings in the database: this operation creates a copy of all the data in Matlab .mat files in the Brainstorm database folders. You could process continuous recordings in the same way, but the .mat format has this limitation that the entire file has to be read even when you want to access just a portion of it. Long recordings usually cannot fit in memory and have to be split in small blocks of a few seconds, which makes it very difficult to review and process.

Brainstorm offers the possibility to visualize continuous MEG/EEG recordings in any of the supported file formats without having to fully "import" them. A link to the native file is created in the database, which can be then manipulated almost like the "imported" recording blocks. Only the description of the file is saved in the database, and when displaying it the values are read directly from the native file.

In addition, an interface allows to edit the time markers that are saved in the file. Those markers can then be used to import the recordings in the database (ie. to do the segmentation of the continuous recordings in epochs/trials). Then the imported epochs/trials (hard copies in .mat format) can be pre-processed and averaged.

From CTF

Channel file

Let's explore what you can do with the first file. Right-click on the CTF channels file and try all the menus.


The menus in the Display menu display the same thing, but in a different way. You can add the scalp (or cortex) surface easily with the toolbar in the Surfaces tab, in the main window (Add a surface "+" button).

channelCtf.gif channelHelmet.gif channelMeg.gif

Display a table with all the information about the individual channels. You can use this window to view and edit the channels properties.


The channel file describes each channel separately, with the following information:

For the moment, the registration between anatomy and sensors is based only on three points that are manually positioned (nasion and ears). This rough alignment technique is quite robust but also very imprecise, and depends on the precision with which the people defined the fiducials, both during the data acquisition and on the MRI slices. For this reason, it is sometimes necessary to correct the position of the sensors.

There is nothing to change here, but remember to always check the registration scalp/sensors just after you import MEG or EEG recordings.

Before locking your subject into that dark shielded room, when you acquire the position of some reference points with a magnetic tracking system (eg. Polhemus Isotrak), it is a good practice to acquire also many other points at the surface of the head. It does not take a very long time but provides very valuable information to register properly the MEG sensors with the MRI and surfaces. The more head points the better, with a minimum of 50 or 100, avoiding the softer parts of the head (cheeks, base of the neck, ears, eyes) because they may have different shapes when the patient is sitting on the MEG chair and when he/she is laying down in the MR scanner. Always insist on the nose, it provides a really good indicator of the orientation of the head.

Note: The digitization of the head shape and the head localization coils with a Polhemus device can be done with Brainstorm: see the digitize tutorial.

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 we saw in 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 2015-02-03 21:44:31 by FrancoisTadel)