Aix-en-Provence, France: October 4, 2021

Half-day workshop, as part of the CuttingEEG conference.

This session will introduce new features for SEEG analysis: iEEG-BIDS specification, MRI segmentation with CAT12, MRI/CT coregistration and non-linear MNI normalization with SPM12, management of anatomical atlases, interactive marking of SEEG electrodes, automatic SEEG contact labelling based on volume and surface parcellations, advanced FEM modeling including DTI-based constraints with DUNEuro. Participants will learn how to access these new tools from the Brainstorm environment on their personal laptops.

General information

Where	Cube classrooms
When	Monday October 4th, 2021: 8:30-12:15
Instructor	Francois Tadel
Audience	Users interested in analyzing sEEG/EEG/ECoG/MEG recordings using Brainstorm. Teaching in English.
Slides	Introduction

Program

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
9:45-10:30	Anatomy Database explorer MRI volumes, surfaces Coregistration of pre- and post-implantation images
10:30-11:30	SEEG recordings Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image Projecting SEEG recordings on MRI and cortex surface
11:30-12:15	Epileptogenicity maps Importing epochs of interest in the database Time-frequency analysis: Identification of ictal HFO frequency bands Computation of epileptogenicity maps: Localization of the seizure onset zone Estimation of the propagation pathways

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Prepare your laptop for the workshop

Setting up the software environment is an important part of the training and is a good preparation step to this workshop. Follow the instructions below if you are insterested in following the hands-on session on your own laptop.

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 Francois Tadel ( francois.tadel@mcgill.ca )