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= Paris, France: December 3-5, 2019 =
Practical workshop on EEG/MEG analysis at ICM, in parallel with FieldTrip and MNE-Python. Program available on the workshop website: http://practicalmeeg2019.org/

The hands-on part of this workshop is based on the Frontiers Research Topic [[https://www.frontiersin.org/research-topics/5158/from-raw-megeeg-to-publication-how-to-perform-megeeg-group-analysis-with-free-academic-software|From raw MEG/EEG to publication]]: a collection of articles processing the [[https://openneuro.org/datasets/ds000117|same multimodal dataset]] using different software environments. We will process together one subject of this dataset, following the processing pipeline described in the article [[https://www.frontiersin.org/articles/10.3389/fnins.2019.00076/full|MEG/EEG Group Analysis With Brainstorm]] and the corresponding [[https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle|online tutorial]].

== General information ==
<<HTML(<TABLE>)>>

<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>>[[http://practicalmeeg2019.org/venue/|ICM]]<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Tuesday Dec 3rd - Thursday Dec 5, 2019: 8:30-17:30<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Instructors'''<<HTML(</TD><TD>)>>[[AboutUs/FrancoisTadel|Francois Tadel]] (Grenoble Institute of Neuroscience)<<BR>>[[http://www.neurotrack.fr/contact/|Anne-Sophie Dubarry]] (Aix-Marseille University)<<BR>>[[https://cognition.ens.fr/fr/member/8648/aurelien-weiss|Aurélien Weiss]] (ENS)<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing sEEG/EEG/ECoG/MEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>>[[https://neuroimage.usc.edu/resources/practicalmeeg2019_brainstorm.pdf|Introduction slides]] | [[http://neuroimage.usc.edu/resources/practicalmeeg2019_brainstorm_walkthrough.pdf|Hands-on walkthrough]] | [[https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_practicalmeeg.m|Processing script]] | [[http://neuroimage.usc.edu/resources/practicalmeeg2019_anatomy_soft.pdf|Anatomy processing]]<<HTML(</TD></TR>)>>

<<HTML(</TABLE>)>>

== Requirements ==
The  participants are required to <<HTML(<FONT color=red>)>> '''bring a laptop''' <<HTML(</FONT>)>>    (an external mouse will add to your comfort). In order to make the    session as efficient as possible, we ask  all the attendees to <<HTML(<FONT color=red>)>>'''download, install and test'''<<HTML(</FONT>)>> the software and sample  dataset on their  laptops prior to the workshop.

Please read carefully the installation instructions: <<BR>>[[https://neuroimage.usc.edu/brainstorm/WorkshopParis2019#Installation_instructions|How to prepare your laptop for the training]]

== Program ==
=== 1. Tuesday am: From raw to ERP ===
 * Introduction to Brainstorm (lecture)
 * Review the MEG+EEG recordings
 * Read and organize events
 * Frequency filters
 * Artifacts detection and cleaning

=== 2. Tuesday pm: Sensor level analysis ===
 * Epoching and averaging
 * Time-frequency analysis

=== 3. Wednesday am:     Creating head and source models ===
 * Import anatomy
 * Registration MRI-sensors
 * Forward model
 * Simulations

=== 4. Wednesday pm:     Single and distributed sources ===
 * MEG noise covariance: From empty room recordings
 * EEG noise covariance: From pre-stimulus baselines
 * Distributed sources / minimum norm estimation
 * Regions of interest
 * LCMV Beamformer
 * Dipole scanning / Volume source models

=== 5. Thursday am:     Group-level analysis ===
 * Project source maps on MNI template
 * Statistical testing
 * Export data to other programs (FieldTrip, SPM, ...)
 * Scripting
 * Example for this workshop: https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_practicalmeeg.m

=== 6. Thursday pm:     User requests ===
 * Bring your own data or prepare your questions

== Installation instructions ==
Before  coming to the workshop, you  need to download  the software and the  tutorial dataset  (1.6 Gb). To streamline   troubleshooting during the  session, please save all the  downloaded   files '''__on your Desktop__'''.

 1. From the Brainstorm [[http://neuroimage.usc.edu/bst/download.php|Download]] page, log in or create a Brainstorm account
 1. Download <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>>   (75 Mb)
 1. If you already have Brainstorm: update it. We need a version released '''after November 18th'''
 1. Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page of this website, and download the file: '''tutorial_practicalmeeg.zip'''
 1. Unzip the two downloaded files on your desktop
 1. Delete the two downloaded zip files
 1. Create a folder "'''brainstorm_db'''" on your '''Desktop '''
 1. Final check: you should have 3 folders on your desktop:
  * '''brainstorm3''': Program folder, with the source code and the compiled executable
  * '''brainstorm_db''': Brainstorm database (empty)
  * '''tutorial_practicalmeeg''': Example dataset used during the training session
 1. Start Brainstorm (see following section)
 1. Select the menu '''Help > Workshop preparation'''.
 1. Follow  the instructions: when you see the 3D figure, make sure you see both a  transparent head surface and a brain surface. Try to rotate the view  with your mouse, and zoom in and out with the mouse wheel. <<BR>><<BR>> {{attachment:test_bst.gif}}
 1. If you want to call FieldTrip functions from Brainstorm (multitaper, cluster-based statistics and dipole fitting), '''download and install FieldTrip''' on your computer:<<BR>>http://www.fieldtriptoolbox.org/download/

== Running Brainstorm for the first time ==
==== With Matlab ====
 1. Matlab versions >= 2014b are faster and produce nicer graphics: consider upgrading if possible
 1. Start Matlab
 1. Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be done automatically
 1. Go to the brainstorm3 folder
 1. Type "brainstorm" in the command window
 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created

==== Without Matlab ====
 1. The instructions below are valid for the following operating systems:
  * '''Windows''': Any version ([[https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/SystemRequirements-Release2015b_Windows.pdf|details]])
  * '''Linux''': Ubuntu 14.04+, RedHat 6.x+, Debian 7.x, SUSE 11.3+  ([[https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/SystemRequirements-Release2015b_Linux.pdf|details]])
  * '''MacOS''': 10.9.5 (Mavericks), 10.10 (Yosemite) ([[https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/SystemRequirements-Release2015b_Macintosh.pdf|details]])
  * If your system is not listed, try another version: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]], [[InstallationR2016a|2016a]], [[InstallationR2016b|2016b]], [[InstallationR2017a|2017a]]
 1. Download the '''MCR R2015b (9.0)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]]
 1. Install the MCR:
  * __Windows__: Double-click on the .exe and follow the instructions
  * __MacOS__: Click on the zip file to unzip it, then click on "InstallForMacOSX"
  * __Linux__: From a terminal, unzip .zip, then run ./install
 1. Run the program in brainstorm3/bin/R2015b/
  * __Windows__: Double-click on ''brainstorm3.bat''
  * __MacOS__: Double-click on ''brainstorm3.command ''and wait for instructions
  * __Linux__: From a terminal, run:<<BR>>''cd brainstorm3/bin/R2015b/''<<BR>>''./brainstorm3.command ''
 1. Troubleshooting for MacOS or Linux:
  * On   recent versions of MacOS, you may get an error message "Application   can't be opened because it is from an unidentified developer". This   message would appear for all the programs that were not downloaded from   the Apple app-store. To go around this verification: right-click on the   application > Open, then click on the Open button.
  * From a terminal, make sure that the file "''brainstorm3.command''" is executable:<<BR>>''chmod a+x brainstorm3.command''
  * If nothing happens, run: <<BR>>''./brainstorm3.command MCR_DIR''<<BR>>MCR_DIR is the MCR 9.0 folder (ex: /Applications/MATLAB/MCR/v90)
  * Try with another binary release: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]], [[InstallationR2016a|2016a]], [[InstallationR2016b|2016b]], [[InstallationR2017a|2017a]]...
 1. Troubleshooting for Windows:
  * Your   current user may not have the necessary privileges. If you are an   administrator for your computer, you can do the following: right-click   on ''brainstorm3.bat'' > Run as administrator.
  * If   you are not the administrator of your computer and Matlab or the MCR   are not installed in the standard paths, Brainstorm may have trouble   finding them. To specify manually the path of the MCR or Matlab folder,   right-click on ''brainstorm3.bat'' > Edit. Fill the second line  of  the script (Example: @SET MATLABROOT="C:\Program  Files\MATLAB\R2015b"),  save the file, and try to execute it again.
 1. On Linux or MacOS, you may be asked to select the folder where you installed the MCR.
 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created.

== Bring your own data ==
The last session will be mostly dedicated to adressing participants' requests.  We encourage you to prepare some  EEG/MEG/ECoG/sEEG data you  would  be  interested in processing with Brainstorm. If you are coming  with colleagues, try to organize small  groups with similar interests  (1-4 people).

The list of file formats that can be read by Brainstorm is available on the [[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|Introduction page]]. Please contact us in advance if you are not sure your dataset can be imported in Brainstorm.

If    you are interested in using the subject's MRI for more realistic   source  estimation, you would have to process it in advance. You could   try  using the following programs: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]], [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT12]]