= Trois-Rivières, Québec, Canada May 7-8, 2024 =
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Practical workshop on EEG/MEG analysis at UQTR

Two-day Brainstorm training, EEG-oriented.<<BR>>During the two days, participants will process an EEG dataset to learn and explore Brainstorm features. In the second 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.uqtr.ca|UQRT ]] <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>> May 7 - 8, 2024: 09:00-17:30<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[#Registration_form|Registration form]] <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>[[https://oraprdnt.uqtr.uquebec.ca/pls/public/genw050r.page_perso?owa_no_personne=121934|Mathieu Piché]]<<BR>> (Université du Québec à Trois-Rivières)<<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 EEG and iEEG recordings using Brainstorm.<<BR>>Some experience with EEG is recommended. Teaching in English.<<BR>>Number of participants: 30 <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[https://mcgill-my.sharepoint.com/:b:/g/personal/raymundo_cassanigonzalez_mcgill_ca/Ef01EfEJC3ZKg4K1AxKhauYBqqm10Ew0Y38vj8JMssRUUA?e=PZPyIl&download=1|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXX|Lectures slides]] | [[https://mcgill-my.sharepoint.com/:b:/g/personal/raymundo_cassanigonzalez_mcgill_ca/Eaqhe2HupwFFml4Bcj8JQhYBwM3N0h6MJdxlr31Hc-n02w?e=UKhGfq&download=1|Walkthrough]] | [[https://forms.gle/ZgBErMFoqZRCkPeBA|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. 

== Installing Brainstorm ==
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 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 a similar processing pipeline as the one 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: '''`ds000117_S1R1.zip`''' (820 MB):<<BR>>
 [[https://mcgill-my.sharepoint.com/:u:/g/personal/raymundo_cassanigonzalez_mcgill_ca/EbzZzdutfsdIknvTsgZuwhQBdZwlSZ0lIEXg5h83ffVJWQ?e=2dVh4f&download=1|Download link]]
 1. Unzip the downloaded file on your desktop: it will create a new folder named `ds000117_S1R1`. It contains raw data for one participant, one run.
 1. Download the tutorial dataset: '''`UQTR_S1S2_R1R2.zip`''' (950 MB):<<BR>>
 [[https://mcgill-my.sharepoint.com/:u:/g/personal/raymundo_cassanigonzalez_mcgill_ca/EVlwwHLj7qxMlYkJpjblRe4BnqHGE2EFmaEzrvjRovlStw?e=QkVngC&download=1|Download link]]
 1. Unzip the downloaded file on your desktop: it will create a new folder named `UQTR_S1S2_R1R2`. It contains pre-processed data for two participants, two runs each.
 1. Final check: after following the steps above, you should have 4 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_S1R1`''': Dataset 1 used during the workshop session
  * '''`UQTR_S1S2_R1R2`''': Dataset 2 used during the workshop session
 
== Program ==
=== Day 1 ===
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<<HTML(<TR><TD>)>>08:30-09:00<<HTML(</TD><TD>)>>'''Onsite assistance in installing the material for the training session'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:00-09:30<<HTML(</TD><TD>)>>'''Biological origins of EEG/MEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:30-10:00<<HTML(</TD><TD>)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:30-12:00<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''

Set anatomy

Review RAW recordings

Manage events

Frequency filters

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<<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:00-16:00<<HTML(</TD><TD>)>>'''Pre-processing and epoching'''

Artifact detection

Artifact correction with ICA and SSP

Import epochs and sensor averages

Statistics, sensor level

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<<HTML(<TR><TD>)>>14:45-15:15<<HTML(</TD><TD>)>> Spectral and '''time-frequency analysis of EEG/MEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>>

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

Time-frequency representation of EEG/MEG signals

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<<HTML(<TR><TD>)>>15:45-16:15<<HTML(</TD><TD>)>>'''Beyond the GUI''' 
Plugins in Brainstorm

Scripting

Collaboration and GitHub

<<HTML(<TR><TD>)>>16:15-16:30<<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>)>>09:45-12:00<<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

Statistics, source level

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<<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:00-14:05<<HTML(</TD><TD>)>>'''Subject level analysis'''

Subject averages (sensor and source levels)

Within subject differences

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<<HTML(<TR><TD>)>>14:05-15:00<<HTML(</TD><TD>)>>'''Group level analysis'''

Preparing sensor and source data

Grand averages

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<<HTML(<TR><TD>)>>15:00-15:45<<HTML(</TD><TD>)>>'''Connectivity''' ''(Lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:45-16:15<<HTML(</TD><TD>)>>'''Connectivity '''

Connectivity scout level

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<<HTML(<TR><TD>)>>16:15-16:30<<HTML(</TD><TD>)>>'''Wrap-up'''

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We provide [[https://mcgill-my.sharepoint.com/:b:/g/personal/raymundo_cassanigonzalez_mcgill_ca/Eaqhe2HupwFFml4Bcj8JQhYBwM3N0h6MJdxlr31Hc-n02w?e=UKhGfq&download=1|a detailed step-by-step walkthrough]] of the data analyses performed during the training.

== Bring your own data ==
If time allows, the last part of the second day will be dedicated to addressing participants' requests.  We encourage you to bring in your own sample of EEG iEEG data that you would be interested in processing with Brainstorm. The file formats that can be read by Brainstorm are listed on the [[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|Introduction page]]. 

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

== Registration form ==
Please register in the form below.

To prep for the hands-on workshop, you will be receiving an email with specific instructions about a week before the event.


<<HTML(<FONT color=red>)>>'''Note: '''<<HTML(</FONT>)>>__The event is now at full capacity__. As such the registration is closed. Thank you for your interest. Keep posted for new workshop announcements.