Live Brainstorm workshop and Q&A, Online: May XX, 2021

Two-hour online Brainstorm workshop and Q&A, live on Zoom.

General information

Where	Zoom (link will provided after registration)
When	*day May XX, 2021: XX:XX-XX:XX EDT
Instructors	Sylvain Baillet (Montreal Neurological Institute / McGill, Canada) Raymundo Cassani (Montreal Neurological Institute / McGill, Canada)
Audience	Open to both beginners and advanced users. Bring your own questions.

Program

This workshop is based on topics presented at detail in the get started tutorials.

Brainstorm overview

• Main user interface
• Software structure
• Typical data workflow

Anatomy data

• Database explorer
• MRI volumes and surfaces
• Default anatomy

Functional data

• Database explorer
• Reviewing recordings
• Visualization of recordings, montages and options
• Events and artifact removal with SSP
• Importing event-related data
• Forward model (head model)
• Inverse problem (source estimation) and normalization
• Visualization of sources, scouts and options

Process tab

• Process1 and Process2
• Overview of process categories
• Pipeline editor
• Process options and online help
• Pipeline as script

Q&A

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Prepare your laptop for the workshop (optional)

Due to time limitation this workshop is not hands-on, thus it is not required to install Brainstorm in your computer. However, if you decide to install Brainstorm and give try before the workshop, follow the instructions below.

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 (110Mb). Additionally, the epileptogenicity analysis is based on SPM12 (100Mb). To streamline troubleshooting during the session, please save all the downloaded files on your Desktop.

1. From the Brainstorm Download page, log in or create a Brainstorm account

2. Download the following files to your Desktop folder:

   • Brainstorm software: brainstorm_YYMMDD.zip (70 Mb)

   • Tutorial dataset: workshop_cuttingeeg.zip (41 Mb)

3. If you already have Brainstorm on your laptop, make sure to update it before coming.

4. Download SPM12 from the UCL website, free registration required:
   http://www.fil.ion.ucl.ac.uk/spm/software/download/

5. Unzip the three downloaded files on your desktop, then delete them

6. Create a folder "brainstorm_db" on your Desktop

7. Final check: you should have now 4 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

   • spm12: SPM toolbox, required for the epileptogenicity analysis

8. Run Brainstorm, make sure it works correctly on your computer (read the next section)

9. Tell Brainstorm where you unzipped SPM12: Menu File > Edit preferences > SPM toolbox.

Running Brainstorm for the first time

With Matlab

1. Matlab versions >= 2014b are faster and produce nicer graphics: consider upgrading if possible

2. Start Matlab

3. Do NOT add brainstorm3 folder to your Matlab path: this will be done automatically

4. Go to the brainstorm3 folder
5. Type "brainstorm" in the command window
6. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created

7. Tell Brainstorm where you unzipped SPM12: Menu File > Edit preferences > SPM toolbox.
   No need to add SPM to the Matlab path either, Brainstorm will do it when needed.

Without Matlab

• The Brainstorm distribution includes a stand-alone version, created with the Matlab Compiler, which can be used without any Matlab license. However, compiled code cannot execute Matlab scripts that are not compiled, which prevents the use of external toolboxes (SPM, FieldTrip).
  
  The last part of this hands-on session will rely on functions from the SPM toolbox, therefore if you use the compiled version, you wouldn't be able to follow the session until the end on your laptop. If you still want to run the compiled version of Brainstorm on your laptop, please refer to the main installation page.

Make sure it works

In order to check if Brainstorm works properly or your computer, please follow these instructions:

• Create a new protocol: Menu File > New protocol.
  Set the name to "Test", don't change the other default options.

• In the folder "Default anatomy", double-click successively on the files: MRI, head, cortex_15002V
• It should open the figures below, make sure they work correctly:
  • Click in the MRI Viewer to move the slices
  • Click+move your mouse in the 3D figure to rotate

  • Zoom in/out with the mouse wheel or the two-finger scroll on MacBook pads

  • The head surface should be transparent, with the brain visible through it

  

Troubleshooting

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

WorkshopZoom2021 (last edited 2021-05-10 19:38:57 by RaymundoCassani)