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Los Angeles, CA, USA: October 18th, 2023

Half-day workshop, as part of the CuttingGrden2023 conference. This session will be an introduction to Brainstorm for EEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops.

General information

Where	Univerisyt of Southern California
When	Wednesday October 18th, 2023: 13:00-17:30
Instructor	Raymundo Cassani & Takfarinas Medani
Registration	Please visit this page.
Audience	Users interested in analyzing EEG/MEG recordings using Brainstorm. Teaching in English.
Documents	Introduction slides \| Walkthrough \| Survey

Requirements

In order to make the workshop as efficient as possible, we ask all the attendees to: download, install and test the software and download the workshop dataset on their laptops prior to the workshop.

Installing Brainstorm

Please read carefully the following instructions on:
preparing your laptop for the training

Workshop dataset

The workshop dataset is a pre-processed version of the dataset in used in the Brainstorm tutorial on median nerve stimulation. It consists of simultaneous EEG and MEG recordings during a median nerve stimulation experiment (right arm). A full description of the dataset can be found here.

Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop.

Download the tutorial dataset (360 MB):
- https://box.bic.mni.mcgill.ca/s/hKO5zc2W4uDE3Zk
Unzip the downloaded file on your desktop: it will create a new folder named workshop_lax
Final check: after following the steps above, you should have 3 folders on your desktop:
- brainstorm3: the software folder, containing the source code and the compiled executable
- brainstorm_db: your Brainstorm database (which should be empty for now)
- workshop_lax: Dataset used during the workshop session

Program

12:30-13:00	Onsite assistance in installing the material for the training session
13:00-13:30	Introduction to Brainstorm (lecture)
13:30-14:35	Loading anatomy and recordings Set anatomy Review RAW recordings Import events
14:35-15:35	Pre-processing Frequency filters Artifact detection Artifact correction with SSP
15:35-15:50	Coffee break
15:50-16:20	Analysis sensor level Import recordings Review trials Trial averages
16:20-16:55	Source estimation Forward model (aka Head model) Noise covariance matrix Source estimation (from EEG and MEG recordings)
16:55-17:15	Analysis source level Cortex parcellations: Atlases and Scouts

We provide a detailed step-by-step walkthrough of the data analyses performed at the training.

Troubleshooting

For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )

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-= 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.
+= Los Angeles, CA, USA: October 18th, 2023 =
Half-day workshop, as part of the [[https://cuttinggardens2023.org/|CuttingGrden2023 conference]]. This session will be an introduction to Brainstorm for EEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops.
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-<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>>[[https://cuttingeeg2021.org/venue/|Cube classrooms]]<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|Univerisyt of Southern California]]<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Monday October 4th, 2021: 8:30-12:15<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Wednesday October 18th, 2023: 13:00-17:30<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>[[AboutUs/FrancoisTadel|Francois Tadel]]<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>[[https://neuroimage.usc.edu/brainstorm/AboutUs/RaymundoCassani|Raymundo Cassani]] & [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani#preview|Takfarinas Medani]]<<HTML(</TD></TR>)>>
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-<<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>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#registration|Please visit this page]]. <<HTML(</TD></TR>)>>
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-<<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>)>>
+<<HTML(<TR><TD>)>>'''Audience'''''' '''<<HTML(</TD><TD>)>>Users interested in analyzing EEG/MEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>>
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+<<HTML(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>>
[[https://box.bic.mni.mcgill.ca/s/XXXXX|Introduction slides]] |  
[[https://box.bic.mni.mcgill.ca/s/XXXXX|Walkthrough]] |
[[https://box.bic.mni.mcgill.ca/s/XXXXX|Survey]]
<<HTML(</TD></TR>)>>
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+== Requirements ==
In order to make the workshop as efficient as possible, we ask all the attendees to: <<HTML(<FONT color=red>)>>'''download, install and test'''<<HTML(</FONT>)>> the software and <<HTML(<FONT color=red>)>>'''download'''<<HTML(</FONT>)>> the workshop dataset on their laptops prior to the workshop.

== Installing Brainstorm ==
Please read carefully the following instructions on: <<BR>>[[WorkshopGeneralInstall|preparing your laptop for the training]]

== Workshop dataset ==
The workshop dataset is a pre-processed version of the dataset in used in the [[Tutorials/Yokogawa|Brainstorm tutorial on median nerve stimulation]]. It consists of simultaneous EEG and MEG recordings during a median nerve stimulation experiment (right arm). A full description of the dataset can be found [[Tutorials/Yokogawa#Description_of_the_experiment|here]].

Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop.

 1. Download the tutorial dataset (360 MB):
  https://box.bic.mni.mcgill.ca/s/hKO5zc2W4uDE3Zk
 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshop_lax`'''
 1. Final check: after following the steps above, you should have 3 folders on your desktop:
  * '''`brainstorm3`''': the software folder, containing the source code and the compiled executable
  * '''`brainstorm_db`''': your Brainstorm database (which should be empty for now)
  * '''`workshop_lax`''': Dataset used during the workshop session
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-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>)>>12:30-13:00<<HTML(</TD><TD>)>>Onsite assistance in installing the material for the training session <<HTML(</TD></TR>)>>
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+Line 48:
-<<HTML(<TR><TD>)>>9:15-9:45<<HTML(</TD><TD>)>>'''Lecture: Brainstorm overview'''
+<<HTML(<TR><TD>)>>13:00-13:30<<HTML(</TD><TD>)>>Introduction to Brainstorm (lecture)<<HTML(</TD></TR>)>>
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+Line 50:
-Software structure, typical data workflow
+<<HTML(<TR><TD>)>>13:30-14:35<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''
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+Line 52:
-Presentation of the example dataset (BIDS-iEEG)
+Set anatomy

Review RAW recordings

Import events
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-<<HTML(<TR><TD>)>>9:45-10:45<<HTML(</TD><TD>)>>'''Anatomy'''
+<<HTML(<TR><TD>)>>14:35-15:35<<HTML(</TD><TD>)>>'''Pre-processing'''
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+Line 62:
-Database explorer
+Frequency filters
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-MRI volumes, surfaces
+Artifact detection
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+Line 66:
-Anatomical parcellations
+Artifact correction with SSP <<HTML(</TD></TR>)>>
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-Coregistration of pre- and post-implantation images<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>15:35-15:50<<HTML(</TD><TD>)>>''Coffee break''<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>10:45-11:45<<HTML(</TD><TD>)>>'''SEEG recordings'''
+<<HTML(</TD></TR>)>>
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+Line 72:
-Reviewing continuous SEEG recordings
+<<HTML(<TR><TD>)>>15:50-16:20<<HTML(</TD><TD>)>>'''Analysis sensor level'''
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-Montages and management of event markers
+Import recordings
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-Marking SEEG contacts on post-implantation image
+Review trials
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-Anatomical labelling of SEEG contacts
+Trial averages
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+Line 80:
-<<HTML(<TR><TD>)>>11:45-12:15<<HTML(</TD><TD>)>>'''Advanced topics - Based on participants' requests'''
+<<HTML(</TD></TR>)>>
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-Time-frequency analysis: Identification of ictal HFO frequency bands
+<<HTML(<TR><TD>)>>16:20-16:55<<HTML(</TD><TD>)>>'''Source estimation'''
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+Line 84:
-Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways
+Forward model (aka Head model)
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+Line 86:
-FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling
+Noise covariance matrix
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+Line 88:
-Open discussion with Bainstorm users
+Source estimation (from EEG and MEG recordings)

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>16:55-17:15<<HTML(</TD><TD>)>>'''Analysis source level'''

Cortex parcellations: Atlases and Scouts
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-<<BR>>

----
= 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}}
+We provide [[https://box.bic.mni.mcgill.ca/s/XXXXX|a detailed step-by-step walkthrough]] of the data analyses performed at the training.
-Line 167:
+Line 103:
-For any technical problem, please contact Francois Tadel ( francois.tadel@mcgill.ca )
+For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )