EEG and epilepsy

This tutorial introduces some concepts that are specific to the management of EEG recordings in the Brainstorm environment. It also describes a standard pipeline for analyzing epilepsy recordings. It is based on clinical case from the Epilepsy Centre, at the University Hospital Freiburg, Germany. The EEG data was recorded at 1024Hz, using a Neurofile NT digital video-EEG system with 128 channels. The anonymized dataset can be downloaded directly from the Brainstorm download page.

The case from this tutorial is also published in this article: Dümpelmann M, Ball T, Schulze-Bonhage A
LORETA allows reliable distributed source reconstruction based on subdural strip and grid recordings, Hum Brain Mapp. 2012

License

This tutorial dataset (EEG and MRI data) remains proprietary of the Epilepsy Centre, University Hospital Freiburg, Germany. Its use and transfer outside the Brainstorm tutorial, e.g. for research purposes, is prohibited without written consent from the Epilepsy Centre in Freiburg. For questions please contact A. Schulze-Bonhage, MD, PhD: andreas.schulze-bonhage@uniklinik-freiburg.de

Presentation of the clinical case

The EEG data was recorded at 1024Hz, using a Neurofile NT digital video-EEG system with 128 channels and a 16-bit A/D converter. The signal was filtered in the recording system with a high-pass filter with a time constant of 1 second and a low-pass filter with a cutoff frequency of 344 Hz. The spikes were visually identified and averaged with the ASA package. The spike average showed prominent peaks in the grid contacts G_A2-4, G_B2-5, G_C1-3.

Type of epilepsy, supposed location, etc.

Download and installation

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

• Go to the Download page of this website, and dowload the file: sample_epilepsy.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 "TutorialEpilepsy" and select the options:

  • "No, use individual anatomy",

  • "Yes, use one channel file per subject".

Import the anatomy

• Create one subject.

• Right-click on the subject node > Import anatomy folder > sample_epilepsy/Anatomy (format=BrainVISA)

• For now the MRI is processed with BrainVISA, but we would like to have it fully processed with FreeSurfer.

• If no anatomy available: Warping tutorial

Access the recordings

• Switch to the "functional data" view.

• Right-click on the subject folder > Review raw file > sample_epilepsy/Data/tutorial_EEG.bin (format = "EEG: Deltamet Neurofile-Coherence (*.bin)")

• Right-click on the subject folder > Import channel file > sample_epilepsy/Data/XensorTest.elc (format = "EEG: ANT Xensor (*.elc)")<<BR>=> Contains the default electrodes positions from the ASA software (ANT).

• Change the sensor type of the following electrodes to MISC: SP1, SP2, RS, PHO, DELR, DELL, QR, QL

• Run the automatic alignment manually.

Mark and review spikes

• How was it done initially?
• How would we do it in Brainstorm?
• Import 177 spikes:

  • [-1, +1] seconds around the spike events (???)

  • Remove DC offset based on the whole trial (-1s to +1s) (???)

Source analysis

• Compute head model: OpenMEEG or 3-shell sphere (???)

• Noise covariance matrix: [-1000, -800] ms from all the imported trials (???)

• Source model: (???)

Tools to be developed for this tutorial

• Set the time resolution of the display figures in seconds per centimeter (s/cm): the length of the page changes automatically with the size of the window.
• Flip +/- the Y axis (already done: check the brainstorm toolbar)