= Brainstorm-FieldTrip auditory tutorial =
''Authors: Francois Tadel, Elizabeth Bock, Robert Oostenveld.<<BR>>''

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 [[http://fieldtrip.fcdonders.nl/|FieldTrip website]].

Note that the operations used here are not detailed, the goal of this tutorial is not to teach Brainstorm to a new inexperienced user. For in depth explanations of the interface and the theory, please refer to the 12+3 introduction tutorials.

<<TableOfContents(2,2)>>

== 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 [[http://neuroimage.usc.edu/brainstorm/CiteBrainstorm|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 [[http://neuroimage.usc.edu/brainstorm3_register/download.php|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 ==
 * Switch to the "anatomy" view.
 * 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=127, y=213, z=139
  * LPA: x=52, y=113, z=96
  * RPA: x=202, y=113, z=91
  * AC: x=127, y=119, z=149
  * PC: x=128, y=93, z=141
  * IH: x=131, y=114, z=206 (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: anatomy.gif

== Access the recordings ==
==== Link the recordings ====
 * Switch to the "functional data" view.
 * Right-click on the subject folder > Review raw file:
  * Select the file format: "'''MEG/EEG: CTF (*.ds...)'''"
  * Select all the .ds folders: '''sample_auditory/data'''

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

== Feedback ==
<<EmbedContent(http://neuroimage.usc.edu/bst/get_feedback.php?Tutorials/Auditory)>>