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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 two days participants will process an EEG/MEG provided dataset to explore Brainstorm and its features. On the last day, participants are encouraged to explore their own data with Brainstorm.

== 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: N <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[TBD|Slides]] | [[TBD|Walkthrough]] | [[TBD|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 ==
Again, we will use pre-installed versions installed on IITB workstations. If you'd llike to use your iwnlaption, please read carefully the following instructions on:<<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 processing the [[https://openneuro.org/datasets/ds000117|same multimodal dataset]] using different software environments. We will process together one subject of this dataset, 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/XXXXXXXXXXXX
 1. Unzip the downloaded file on your desktop
 1. Final check: you should have 3 folders on your desktop:
  * '''`brainstorm3`''': Program folder, with the source code and the compiled executable
  * '''`brainstorm_db`''': Brainstorm database (empty)
  * '''`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>)>>'''Time-frequency analysis of 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>)>>'''Source estimation theory''' ''(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>)>>'''Analysis Subject level'''

Statistical testing

Subject averages (sensors, time-frequency and sources)

With-in subject differences

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

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/9BXiGy7WpKhgnxu|a detailed step-by-step walkthrough]] of the data analyses performed at 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, we will cover more aspects of the software with the tutorial dataset used in the present workshop.