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Los Angeles, CA, USA: October 19, 2023

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

General information

Where	Univerisyt of Southern California
When	Wednesday October 19th, 2023: 13:00-17:30
Instructor	Raymundo Cassani & Takfarinas MEDANI
Audience	Users interested in analyzing EEG/MEG recordings using Brainstorm. Teaching in English.
Documents	Introduction slides \| Tutorial walkthrough

Program (TBD)

This session is based on a simplified version of the SEEG/Epileptogenicity tutorial.

8:30-9:15	Onsite assistance in installing the material for the training session
9:15-9:45	Lecture: Brainstorm overview Software structure, typical data workflow Presentation of the example dataset (BIDS-iEEG)
9:45-10:45	Anatomy Database explorer MRI volumes, surfaces Anatomical parcellations Coregistration of pre- and post-implantation images
10:45-11:45	SEEG recordings Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image Anatomical labelling of SEEG contacts
11:45-12:15	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

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.

Go to the Download page, complete the quick and free registration process.
If you don't receive the confirmation email, please check your spam folder.
Download the following files to your Desktop folder:
- Brainstorm software: brainstorm_YYMMDD.zip (source+binary, 90 Mb)
- Tutorial dataset: workshop_cuttingeeg.zip (162 Mb)
If you already have Brainstorm on your laptop, make sure to update it before coming.
Unzip the two downloaded files on your desktop, then delete them
Create a folder "brainstorm_db" on your Desktop
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
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)

Start Matlab
Do NOT add brainstorm3 folder to your Matlab path: this will be done automatically
Go to the brainstorm3 folder
Type "brainstorm" in the command window
When asked for the database folder, pick the "brainstorm_db" you have just created
Install SPM12: Menu Plugins > spm12 > Install.

Without Matlab

Install the Matlab Runtime R2020a (9.8): Mathworks website
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:
  cd brainstorm3/bin/R2020a/
  ./brainstorm3.command
For troubleshooting, see the 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.

Troubleshooting

For any technical problem, please contact Francois Tadel ( francois.tadel@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 19, 2023 =
Half-day workshop, as part of the [[https://cuttinggardens2023.org/|CuttingGrden conference]]. This session will be an introduction to Brainstorm for EEG analysis. Participants will learn how to use Brainstorm and acces 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 19th, 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>)>>[[AboutUs/FrancoisTadel|Raymundo Cassani & 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>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing  EEG/MEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>>
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-== Program ==
+== Program (TBD) ==
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- *
 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"'''.
+ * 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"'''.
-Line 76:
+Line 75:
- *
 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.
+ * 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.
-Line 79:
+Line 77:
- *
 Don't forget your '''power adapter'''!
+ * Don't forget your '''power adapter'''!
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+Line 82:
-.
 Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page, complete the quick and free registration process.
+. Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page, complete the quick and free registration process.
-Line 89:
+Line 84:
-.
 If you don't receive the confirmation email, please check your '''spam folder'''.
+. If you don't receive the confirmation email, please check your '''spam folder'''.
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+Line 86:
+. Download the following files to '''your Desktop''' '''folder''':
  * '''Brainstorm software''': <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>>   (source+binary, 90 Mb)
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-.
 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)
+  * '''Tutorial dataset''': <<HTML(<FONT color=red>)>>workshop_cuttingeeg.zip<<HTML(</FONT>)>>  (162 Mb)
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+Line 93:
-.
 Create a folder "'''brainstorm_db'''" on your '''Desktop '''
+. Create a folder "'''brainstorm_db'''" on your '''Desktop '''
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+Line 96:
-  *
  '''brainstorm3''': Program folder, with the source code and the compiled executable
+  * '''brainstorm3''': Program folder, with the source code and the compiled executable
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+Line 98:
-  *
  '''brainstorm_db''': Brainstorm database (empty)
+  * '''brainstorm_db''': Brainstorm database (empty)
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+Line 100:
-  *
  '''workshop_cuttingeeg''': Example dataset used during the training session
+  * '''workshop_cuttingeeg''': Example dataset used during the training session
-Line 127:
+Line 110:
-.
 Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be done automatically
+. Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be done automatically
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+Line 115:
-.
 '''Install SPM12''': Menu Plugins > spm12 > Install.
+. '''Install SPM12''': Menu Plugins > spm12 > Install.
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+Line 118:
-.
 Install the Matlab Runtime '''R2020a (9.8)''': [[https://www.mathworks.com/products/compiler/matlab-runtime.html|Mathworks website]]
+. Install the Matlab Runtime '''R2020a (9.8)''': [[https://www.mathworks.com/products/compiler/matlab-runtime.html|Mathworks website]]
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+Line 121:
-  *
  Windows: Double-click on ''brainstorm3.bat''
+  * Windows: Double-click on ''brainstorm3.bat''
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+Line 123:
-  *
  MacOS: Double-click on ''brainstorm3.command ''and wait for instructions
+  * MacOS: Double-click on ''brainstorm3.command ''and wait for instructions
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+Line 125:
-  *
  Linux: From a terminal, run:<<BR>>''cd brainstorm3/bin/R2020a/<<BR>>'' ''./brainstorm3.command ''
+  * Linux: From a terminal, run:<<BR>>''cd brainstorm3/bin/R2020a/<<BR>>'' ''./brainstorm3.command ''
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+Line 127:
-.
 For troubleshooting, see the [[https://neuroimage.usc.edu/brainstorm/Installation#Start_Brainstorm|Installation]] page.
+. For troubleshooting, see the [[https://neuroimage.usc.edu/brainstorm/Installation#Start_Brainstorm|Installation]] page.
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+Line 132:
- *
 Select the menu: '''Help > Workshop preparation'''.
+ * Select the menu: '''Help > Workshop preparation'''.
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- *
 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}}
+ * 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}}