## page was renamed from Tutorials/DuneuroMunsterData
'''[TUTORIAL UNDER CONSTRUCTION]'''

Will be completed soon

In this tutorial we describe the full FEM process as described in the SPIE paper

We may keep the previous tutorial as a basic and this tutorial is an advanced version.



= FEM tutorial: MEG/EEG Median nerve stimulation =
''Authors: Takfarinas Medani,,,''

This tutorial introduces the FEM modeling in the Brainstorm environment.

Note that the operations used here are not detailed, the goal of this tutorial is not to introduce Brainstorm to new users. For in-depth explanations of the interface and theoretical foundations, please refer to the [[http://neuroimage.usc.edu/brainstorm/Tutorials#Get_started|introduction tutorials]].

<<TableOfContents(3,2)>>

== 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:

 * Right median nerves were percutaneously stimulated using monophasic square-wave impulses with a duration of 0.3 ms at 2.8 Hz.
 * The stimulus intensity was set at the motor threshold to evoke mild twitches of the thumb.
 * The stimulus onsets were recorded as low-to-high TTL with a trigger channel labeled as "Trigger01".
 * The total number of stimuli in the dataset was 336.
 * The MEG data was recorded with a sampling rate of 2000 Hz and a bandpass filter at 0.16-500 Hz with a Yokogawa 160 axial gradiometer system at Yokogawa Electric Corporation, Kanazawa, Japan.
 * The EEG data was recorded with a NIHON KOHDEN system simultaneously with the MEG recordings.

== Export recordings from fif files? ==
==== Full head shape in the the digitizer file ====
In order to realize a precise MRI registration or for warping the default anatomy, you should collect 100 to 200 points describing the entire head shape in addition to the 8 Yokogawa/KIT standard stylus points. To import additional digitized points, follow the instruction below:

 * When digitizing head points:
  * Pick the 8 standard stylus points
  * Pick additional 100 to 200 head points, so that the selected points cover the entire head
 * Edit the digitizer label file (DigitizeLabel.txt) which is used in "Third-party export" so that it defines the 8 points and the additional points.

== Download and installation ==
 * Requirements: You have already followed all the introduction tutorials and you have a working copy of Brainstorm installed on your computer.
 * Start Brainstorm (Matlab scripts or stand-alone version)
 *   * "'''No, use individual anatomy'''",
  * "'''No, use one channel file per condition'''".

== Import the anatomy ==
 * Right-click on the TutorialYokogawa 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"
  * Number of vertices of the cortex surface: 15000 (default value)
 * Click on the link "'''Click here to compute MNI transformation'''".
 * Set the 6 required fiducial points (indicated in MRI coordinates):
  *
 * At the end of the process, make sure that the file "cortex_15000V" is selected (downsampled pial surface, which will be used for the source estimation). If it is not, double-click on it to select it as the default cortex surface.<<BR>><<BR>>

== Access the recordings ==
=== Link the recordings ===
 * Switch to the "functional data" view, the middle button in the toolbar above the database explorer.
 * Right-click on the subject folder > '''Review raw file''':
  *

=== Prepare the channel file ===
 *

=== Refine the MRI registration ===
 *
 *

=== Read the stimulation information ===
 *

== Pre-processing ==
=== Evaluate the recordings ===
 *

=== Frequency filters ===
 *

== Review the recordings ==
=== MEG: Default montages ===

=== MEG: Bad channels ===
 *

=== EEG: Average reference ===
 *

== Artifacts cleaning with ICA ==
=== Detect heartbeats and blinks ===
 *

=== EEG: Heartbeats and eye movements ===
 *
 *

=== MEG: Heartbeats and eye movements ===
 *

== Epoching and averaging ==
=== Import the recordings ===

=== Averaging ===
 *

== Source estimation ==
=== Head model ===
 *

=== Noise covariance matrix ===
 *

=== Inverse model ===
 *
 *
 *

=== Regions of interest ===
 * Create two scouts S1 and S2 to represent the primary and secondary somatosensory cortex of the left hemisphere.
  *

== Scripting ==