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= Mumbai, India June 28-30, 2023 =
Practical workshop on EEG/MEG analysis at IIT Bombay.

Three-day Brainstorm training, EEG- and MEG-oriented.<<BR>>During the first two days, participants will process an EEG/MEG dataset to learn and explore Brainstorm features. On the last day, participants are encouraged to bring their own data, which we will review in small groups.

== General information ==
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<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>>[[https://www.iitb.ac.in/|IIT Bombay]] <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Wednesday, June 28 - Friday 30, 2023 2023: 09:00-17:30<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Instructors'''<<HTML(</TD><TD>)>>[[AboutUs/SylvainBaillet|Sylvain Baillet]] and [[AboutUs/RaymundoCassani|Raymundo Cassani]] <<BR>> (Montreal Neurological Institute / McGill, Canada)<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing MEG/EEG/sEEG recordings using Brainstorm.<<BR>>Some experience with MEG/EEG is recommended. Teaching in English.<<BR>>Number of participants: 30 <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/Ne14TbZdUPlKX1n|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/X1CaQHE9JV6BWN9|Lectures slides]] | [[https://box.bic.mni.mcgill.ca/s/Z1ZWryzcTTaC79e|Walkthrough]] | [[https://forms.gle/sWNCLJ42Q9NtgkFNA|Survey]]<<HTML(</TD></TR>)>>

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== 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. Please note that this session will be run on workstations available at the IITB.

== Installing Brainstorm ==
We will use pre-installed versions installed on IITB workstations. If you would like to use your own laptop, please read carefully the following instructions:<<BR>>[[WorkshopGeneralInstall|preparing your laptop for the training]]

== Workshop dataset ==
The workshop dataset is based on the Frontiers Research Topic [[https://www.frontiersin.org/research-topics/5158/from-raw-megeeg-to-publication-how-to-perform-megeeg-group-analysis-with-free-academic-software|From raw MEG/EEG to publication]]: a collection of articles reporting the analysis of the [[https://openneuro.org/datasets/ds000117|same multimodal dataset]] using different software environments. During this workshop, we will go through the main processing steps using data from of the participants, following the processing pipeline described in the article [[https://www.frontiersin.org/articles/10.3389/fnins.2019.00076/full|MEG/EEG Group Analysis With Brainstorm]] and the corresponding [[https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle|online tutorial]].

Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop.

 1. Download the tutorial dataset (5 GB):
 https://box.bic.mni.mcgill.ca/s/iNxszVo7q8rSXwB
 1. Unzip the downloaded file on your desktop: it will create a new folder named ds000117-iitbombay.
 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)
  * '''`ds000117-iitbombay`''': Dataset used during the workshop session

== Program ==
=== Day 1 ===
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<<HTML(<TR><TD>)>>09:00-09:45<<HTML(</TD><TD>)>>'''Biological origins of EEG/MEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:45-10:30<<HTML(</TD><TD>)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:30-12:30<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''

Set anatomy

Review RAW recordings

Manage events

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<<HTML(<TR><TD>)>>12:30-14:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>14:00-16:00<<HTML(</TD><TD>)>>'''Pre-processing and epoching'''

Frequency filters

Artifact detection

Artifact correction with ICA and SSP

Import epochs and sensor averages

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<<HTML(<TR><TD>)>>16:00-16:45<<HTML(</TD><TD>)>> Spectral and '''time-frequency analysis of EEG/MEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>16:45-17:15<<HTML(</TD><TD>)>>'''Time-frequency analysis'''

Time-frequency representation of EEG/MEG signals

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<<HTML(<TR><TD>)>>17:15-17:30<<HTML(</TD><TD>)>>'''Wrap-up'''

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=== Day 2 ===
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<<HTML(<TR><TD>)>>09:00-09:45<<HTML(</TD><TD>)>>'''Foundations of''' '''source estimation '''''(Lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:45-12:30<<HTML(</TD><TD>)>>'''Sources estimation '''

Forward model (aka Head model)

Noise covariance matrix

Source estimation (surfaces and volume source spaces)

Cortex parcellations: Atlases and Scouts

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<<HTML(<TR><TD>)>>12:30-14:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>14:00-16:00<<HTML(</TD><TD>)>>'''Subject level analysis'''

Statistical testing

Subject averages (sensors, time-frequency and sources)

Within subject differences

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<<HTML(<TR><TD>)>>16:00-17:15<<HTML(</TD><TD>)>>'''Group level analysis'''

Preparing sensor, time-frequency and sources data

Head modelling, cortical source reconstruction

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<<HTML(<TR><TD>)>>17:15-17:30<<HTML(</TD><TD>)>>'''Wrap-up'''

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=== Day 3 ===
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<<HTML(<TR><TD>)>>09:00-10:00<<HTML(</TD><TD>)>>'''Beyond the GUI''' Report viewer

Scripting

Plugins

GitHub

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<<HTML(<TR><TD>)>>09:00-12:30<<HTML(</TD><TD>)>>'''Participants working with their own data'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>12:30-14:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>14:00-17:15<<HTML(</TD><TD>)>>'''Participants working with their own data'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>17:15-17:30<<HTML(</TD><TD>)>>'''Wrap-up'''

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We provide [[https://box.bic.mni.mcgill.ca/s/Z1ZWryzcTTaC79e|a detailed step-by-step walkthrough]] of the data analyses performed during the training.

== Bring your own data ==
The last session will be mostly dedicated to addressing participants' requests.  We encourage you to bring in your own sample of EEG/MEG/ECoG/sEEG data that you would be interested in processing with Brainstorm. We may ask that you pair with other attendees, for logistics purposes.

The file formats that can be read by Brainstorm are listed on the [[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|Introduction page]]. Please contact us in advance if you are not sure your dataset can be imported in Brainstorm. If you do not have data available, you may continue to use the tutorial dataset used in the present workshop.