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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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-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 acces its new tools on their personal laptops.
+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>)>>'''Documents'''<<HTML(</TD><TD>)>> TBD [[https://neuroimage.usc.edu/resources/cuttingeeg2021_brainstorm_slides.pdf|Introduction slides]]  | TBD [[https://neuroimage.usc.edu/resources/cuttingeeg2021_brainstorm_walkthrough.pdf|Tutorial walkthrough]] <<HTML(</TD></TR>)>>

<<HTML(</TABLE>)>>
+<<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>)>> <<HTML(</TABLE>)>>
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 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.
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-Please read carefully the following instructions on:
<<BR>>[[WorkshopGeneralInstall|preparing your laptop for the training]]
+Please read carefully the following instructions on: <<BR>>[[WorkshopGeneralInstall|preparing your laptop for the training]]
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- https://box.bic.mni.mcgill.ca/s/iNxszVo7q8rSXwB
 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshop_lax`'''.
+  . 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`'''
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-<<HTML(<TR><TD>)>>13:00-13:45<<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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-<<HTML(<TR><TD>)>>13:45-14:15<<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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-Software structure, typical data workflow
+<<HTML(<TR><TD>)>>13:30-14:35<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''

Set anatomy

Review RAW recordings

Import events
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-<<HTML(<TR><TD>)>>14:45-15:45<<HTML(</TD><TD>)>>'''Anatomy'''
+<<HTML(<TR><TD>)>>14:35-15:35<<HTML(</TD><TD>)>>'''Pre-processing'''
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-Database explorer
+Frequency filters
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-MRI volumes, surfaces
+Artifact detection
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-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>)>>15:45-16:45<<HTML(</TD><TD>)>>'''EEG recordings'''
+<<HTML(</TD></TR>)>>
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-Reviewing continuous EEG 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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-<<HTML(<TR><TD>)>>16:45-17:45<<HTML(</TD><TD>)>>'''Advanced topics - Based on participants' requests'''
+Review trials
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-Time-frequency analysis: Identification of ictal HFO frequency bands
+Trial averages
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-Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways
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-FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling
+<<HTML(<TR><TD>)>>16:20-16:55<<HTML(</TD><TD>)>>'''Source estimation'''
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-Open discussion with Bainstorm users
+Forward model (aka Head model)

Noise covariance matrix

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