Yokogawa/KIT tutorial

Authors: Francois Tadel, Ei-ichi Okumura, Takashi Asakawa.

This tutorial introduces some concepts that are specific to the management of MEG/EEG files recorded with Yokogawa/KIT systems in the Brainstorm environment.

License

This tutorial dataset (MEG/EEG and MRI data) remains proprietary of Yokogawa Electric Corporation, Japan. Its use and transfer outside the Brainstorm tutorial, e.g. for research purposes, is prohibited without written consent from Yokogawa Electric Corporation.

Description of the experiment

This tutorial is based on a simple median nerve stimulation experiment:

Export recordings from Meg160

Yokogawa/KIT data

To import Yokogawa/KIT data files (.con, .raw, .ave) into Brainstorm, a data export process is required beforehand. The data export function is available in Meg160, which is data analysis software equipped in most of Yokogawa/KIT systems.

If your software does not support the functions used below, please contact Yokogawa via http://www.yokogawa.com/me/index.htm

Preparation

If a wave data file and the corresponding digitizer file are ready for use, there is no additional operation required. Go to "Data export".

If no digitizer file is available, you need first to extract the head surface points:

Data export

The dataset used in this tutorial has been exported from Meg160 using this procedure.

Download and installation

Import the anatomy

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

Access the recordings

Prepare the channel file

Register electrodes with MRI

Review EEG recordings

Import the spike markers

Some spikes were marked by the epileptologists at the Epilepsy Center in Freiburg with Brainstorm and saved in an external text file. We are going to import this file manually.

Pre-process recordings

Evaluation

Two of the typical pre-processing steps consist in getting rid of the contamination due to the power lines (50 Hz or 60Hz) and of the frequencies we are not interested in (a low-pass filter to remove the high-frequencies and a high-pass filter to remove the very slow components of the signals). Let's start with the spectral evaluation of this file.

High-pass filter

We would like to apply a 0.5Hz high-pass filter to the entire file in order to get rid of the long amplitude fluctuations (longer than 2s). With some MEG file formats, Brainstorm supports the creation of new filtered files in native formats, which means that you can drag and grop directly the "Link to raw file" to the Process1 tab and run the band-pass filter process. Unfortunately, this is currently not supported for the file format we are currently working on (Deltamed Coherence-Neurofile).

There is an alternative option which consists in importing the entire continuous file in the database in one single block, then run the filter on it. This approach works is possible only on rather small files (4 * file size < memory on the computer). Here the file size is less than 80 Mb, so it can be easily processed this way.

Epoching and averaging

Import recordings

Average spikes

Source analysis

Head model

Noise covariance matrix

Inverse model

Regions of interest

Z-score normalization

A good way to reveal better the source activity at the cortex level is to calculate a Z-score of the source maps with respect with a quiet baseline. We can use the same baseline as for the calculation of the noise covariance matrix.

Scripting

To reproduce this entire analysis with a script, use the following processes:

Graphic edition

[ATTACH]

Generate Matlab script

This list of processes can be converted automatically to a Matlab script.
See the results on the page: ?EEG and epilepsy: Script.

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Tutorials/Yokogawa (last edited 2014-03-19 21:35:10 by wpa069125)