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

Half-day workshop, as part of the CuttingGardens2023 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. The link to the video will be uploaded soon.

General information

Where	University of Southern California
When	Wednesday October 18th, 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 \| 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. In addition, results obtained in this workshop can be replicated with this script.

Troubleshooting

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

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+## page was renamed from WorkshopLA2023
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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.
+<<HTML(<img align="right" alt="cutting_lax_logo.png" class="attachment" src="/brainstorm/WorkshopLA2023?action=AttachFile&amp;do=get&amp;target=cutting_lax_logo.png" title="cutting_lax_logo.png" style="width: 35%;">)>>

Half-day workshop, as part of the [[https://cuttinggardens2023.org/|CuttingGardens2023 conference]]. <<BR>> 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.  The link to the video will be uploaded soon.
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-<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|Univerisyt of Southern California]]<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]]<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#registration|Please visit this page]]. <<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>)>> 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(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/XRahw8lOSpgFetj|Introduction slides]] |   [[https://box.bic.mni.mcgill.ca/s/rpkrUdfXUSxjArh|Walkthrough]] | [[https://forms.gle/R4g5w1A3aUNz8jMB9|Survey]] <<HTML(</TD></TR>)>> <<HTML(</TABLE>)>>
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-<<HTML(</TABLE>)>>
+== 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.
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-== Program (TBD) ==
This session is based on a simplified version of the xxxx
+== Installing Brainstorm ==
Please read carefully the following instructions on: <<BR>>[[WorkshopGeneralInstall|preparing your laptop for the training]]
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+== 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

== Program ==
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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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+Line 60:
-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
+<<HTML(</TD></TR>)>>
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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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+Line 82:
-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>>

----

== Requirements ==
In order to make the workshop as efficient as possible, we ask all the attendees to prepare their laptops by:

 1. '''Installing''' and '''testing''' Brainstorm in your laptop, and 
 2. '''Downloading''' the workshop dataset prior to the workshop. 

== 1. Install Brainstorm  ==
Please read carefully the following instructions to <<HTML(<FONT color=red>)>>'''download'''<<HTML(</FONT>)>>, <<HTML(<FONT color=red>)>>'''install'''<<HTML(</FONT>)>> and <<HTML(<FONT color=red>)>>'''test'''<<HTML(</FONT>)>> Brainstorm: <<BR>>[[WorkshopGeneralInstall|Preparing your laptop for the training]]

== 2. Workshop dataset ==
TBD.
+We provide [[https://box.bic.mni.mcgill.ca/s/rpkrUdfXUSxjArh|a detailed step-by-step walkthrough]] of the data analyses performed at the training. In addition, results obtained in this workshop can be replicated with [[https://box.bic.mni.mcgill.ca/s/kYKqad5wzYabzq1|this script]].