= Aix-en-Provence, France: October 4, 2021 =
Half-day workshop, as part of the [[https://cuttingeeg2021.org/|CuttingEEG conference]]. This session will introduce new features for SEEG analysis. Participants will learn how to access these new tools from  the Brainstorm environment on their personal laptops.

== General information ==
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<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>>[[https://cuttingeeg2021.org/venue/|Cube classrooms]]<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Monday October 4th, 2021: 8:30-12:15<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>[[AboutUs/FrancoisTadel|Francois Tadel]]<<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/cuttingeeg2021_brainstorm_slides.pdf|Introduction slides]]  | [[https://neuroimage.usc.edu/resources/cuttingeeg2021_brainstorm_walkthrough.pdf|Tutorial walkthrough]] <<HTML(</TD></TR>)>>

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== Program (TBA) ==
This session is based on a simplified version of the [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity|SEEG/Epileptogenicity tutorial]].

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<<HTML(<TR><TD>)>>8:30-9:15<<HTML(</TD><TD>)>>Onsite assistance in installing the material for the training session <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>9:15-9:45<<HTML(</TD><TD>)>>'''Lecture: Brainstorm overview'''

Software structure, typical data workflow

Presentation of the example dataset (BIDS-iEEG)

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<<HTML(<TR><TD>)>>9:45-10:45<<HTML(</TD><TD>)>>'''Anatomy'''

Database explorer

MRI volumes, surfaces

Anatomical parcellations

Coregistration of pre- and post-implantation images<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:45-11:45<<HTML(</TD><TD>)>>'''SEEG recordings'''

Reviewing continuous SEEG recordings

Montages and management of event markers

Marking SEEG contacts on post-implantation image

Anatomical labelling of SEEG contacts

<<HTML(<TR><TD>)>>11:45-12:15<<HTML(</TD><TD>)>>'''Advanced topics - Based on participants' requests'''

Time-frequency analysis: Identification of ictal HFO frequency bands

Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways

FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling

Open discussion with Bainstorm users

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= Prepare your laptop for the workshop =
== Important notes ==
 * Working  with MEG/EEG/SEEG recordings involves a lot of computational resources and  large display windows. Therefore we recommend that you bring a laptop  with a decent processing capacity, '''4Gb RAM''', a '''64bit''' operating system, and a '''screen larger than 13"'''.
 * You  would add to your comfort by bringing an '''external mouse'''.   Most of  the manipulations are done with the mouse, and some involve  an  intensive  use of the mouse wheel/scrolling.
 * Don't forget your '''power adapter'''!

== Installation instructions ==
Before   coming to the workshop, you  need to download  the software and the   tutorial dataset from the  Brainstorm website  (200Mb). To streamline  troubleshooting during the  session, please save all the  downloaded  files '''__on your Desktop__'''.

 1. Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page, complete the quick and free registration process.
 1. If you don't receive the confirmation email, please check your '''spam folder'''.

 1. Download the following files to '''your Desktop''' '''folder''':
  * '''Brainstorm software''': <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>>   (source+binary, 90 Mb)
  * '''Tutorial dataset''': <<HTML(<FONT color=red>)>>workshop_cuttingeeg.zip<<HTML(</FONT>)>>  (162 Mb)
 1. If you already have Brainstorm on your laptop, make sure to update it before coming.
 1. Unzip the two downloaded files on your desktop, then delete them
 1. Create a folder "'''brainstorm_db'''" on your '''Desktop '''
 1. Final check: you should have now 3 folders on your desktop:
  * '''brainstorm3''': Program folder, with the source code and the compiled executable
  * '''brainstorm_db''': Brainstorm database (empty)
  * '''workshop_cuttingeeg''': Example dataset used during the training session
 1. Run Brainstorm, make sure it works correctly on your computer (see next sections)

== Running Brainstorm for the first time ==
If you don't have a Matlab license, you can get a temporary one for the duration of the conference: https://cuttingeeg2021.lpl-aix.fr/t/matlab-installation-licenses-available/151

==== With Matlab (2014b minimum) ====
 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 database folder, pick the "brainstorm_db" you have just created
 1. '''Install SPM12''': Menu Plugins > spm12 > Install.

==== Without Matlab ====
 1. Install the Matlab Runtime '''R2020a (9.8)''': [[https://www.mathworks.com/products/compiler/matlab-runtime.html|Mathworks website]]
 1. Run the program in brainstorm3/bin/R2020a/
  * 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/R2020a/<<BR>>'' ''./brainstorm3.command ''
 1. For troubleshooting, see the [[https://neuroimage.usc.edu/brainstorm/Installation#Start_Brainstorm|Installation]] page.

== Make sure it works ==
To make sure Brainstorm works properly or your computer:

 * Select the menu: '''Help > Workshop preparation'''.
 * 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 or two-finger pad scroll. <<BR>><<BR>> {{attachment:bst_test_2021.png}}

== Troubleshooting ==
For any technical problem, please contact Francois Tadel ( francois.tadel@mcgill.ca )