Brainstorm-FieldTrip auditory tutorial

Authors: Francois Tadel, Elizabeth Bock, Robert Oostenveld.

The aim of this tutorial is to provide high-quality recordings of a simple auditory stimulation and illustrate the best possible analysis paths with Brainstorm and FieldTrip. This page presents the workflow in the Brainstorm environment, the equivalent documentation for the FieldTrip environment is available on the !FieldTrip website.

License

This tutorial dataset (EEG 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

Experiment

• 1 acquisition run = 200 regular beeps + 40 easy deviant beeps
• Random inter-stimulus interval: between 0.7s and 1.7s seconds, uniformly distributed
• The subject presses a button when detecting a deviant
• We would record three runs (each of them is ~5min long), asking the subject to move a bit between the runs (not too much), if we want to test later some sensor-level co-registration algorithms.
• Auditory stim generated with the Matlab Psychophysics Toolbox
• Only one subject

MEG acquisition

• Acquisition at 2400Hz, with a CTF 275 system at the MNI, subject in seating position
• Online 300Hz low-pass filter, files saved with the 3rd order gradient
• Recorded Channels:

• 2 runs: => To test registration algorithms

• run1 - marked a few trials bad => Use for the main example

• run2 - saccades, see component screenshot, they are not really detected well with the auto detection => To illustrate how to remove saccades. External file of marked saccades

• Noise recordings: 30s

• 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 (http://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize)

• 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 - the red point I placed on that ear image we have on both websites)
• Around 150 head points distributed on the hard parts of the head (no soft tissues)

Subject anatomy

• Subject with 1.5T MRI
• Marker on the left cheek

• Processed with FreeSurfer 5.3

Download and installation

• Requirements: You have already followed all the basic tutorials and you have a working copy of Brainstorm installed on your computer.

• Go to the Download page of this website, and download the file: sample_auditory.zip

• Unzip it in a folder that is not in any of the Brainstorm folders (program folder or database folder). This is really important that you always keep your original data files in a separate folder: the program folder can be deleted when updating the software, and the contents of the database folder is supposed to be manipulated only by the program itself.
• Start Brainstorm (Matlab scripts or stand-alone version)

• Select the menu File > Create new protocol. Name it "TutorialAuditory" and select the options:

  • "No, use individual anatomy",

  • "No, use one channel file per condition".

Import the anatomy

• Right-click on the TutorialAuditory folder > New subject > Subject01

  • Leave the default options you set for the protocol

• Right-click on the subject node > Import anatomy folder:

  • Set the file format: "FreeSurfer folder"

  • Select the folder: sample_auditory/anatomy

  • Number of vertices of the cortex surface: 15000 (default value)
• Set the 6 required fiducial points (indicated in MRI coordinates):
  • NAS: x=135, y=222, z=75
  • LPA: x=57, y=118, z=68
  • RPA: x=204, y=119, z=76
  • AC: x=131, y=145, z=110
  • PC: x=130, y=119, z=111
  • IH: x=128, y=134, z=170 (anywhere on the midsagittal plane)
• At the end of the process, make sure that the file "cortex_15000V" is selected (downsampled pial surface, that will be used for the source estimation). If it is not, double-click on it to select it as the default cortex surface.

=> SCREEN CAPTURE

Without the individual MRI

If you do not have access to an individual MR scan of the subject (or if its quality is too low to be processed with FreeSurfer), but if you have digitized the head shape of the subject using a tracking system, you have an alternative: deform one of the Brainstorm templates (Colin27 or ICBM152) to match the shape of the subject's head.

• For more information, read the following tutorial: Warping default anatomy

Discussion

Discussion about the choice of the dataset on the FieldTrip bug tracker:
http://bugzilla.fcdonders.nl/show_bug.cgi?id=2300

Feedback

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