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Trois-Rivières, Québec, Canada May 7-8, 2024

Practical workshop on EEG/MEG analysis at UQTR

Two-day Brainstorm training, EEG-oriented.
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

Where	UQRT
When	May 7 - 8, 2024: 09:00-17:30
Registration	Registration form
Organizers	Mathieu Piché (Université du Québec à Trois-Rivières)
Instructors	Sylvain Baillet and Raymundo Cassani (Montreal Neurological Institute / McGill, Canada)
Audience	Users interested in analyzing EEG and iEEG recordings using Brainstorm. Some experience with EEG is recommended. Teaching in English. Number of participants: 30
Slides	Intro slides \| Lectures 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 based on the Frontiers Research Topic From raw MEG/EEG to publication: a collection of articles reporting the analysis of the 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 MEG/EEG Group Analysis With Brainstorm and the corresponding online tutorial.

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

Download the tutorial dataset: ds000117_S1R1.zip (820 MB):
Download link
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.
Download the tutorial dataset: UQTR_S1S2_R1R2.zip (950 MB):
Download link
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.
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

08:30-09:00	Onsite assistance in installing the material for the training session
09:00-09:30	Biological origins of EEG/MEG signals (lecture S. Baillet)
09:30-10:00	Introduction to Brainstorm (lecture R. Cassani)
10:30-12:00	Loading anatomy and recordings Set anatomy Review RAW recordings Manage events Frequency filters
12:00-13:00	Lunch
13:00-16:00	Pre-processing and epoching Artifact detection Artifact correction with ICA and SSP Import epochs and sensor averages Statistics, sensor level
14:45-15:15	Spectral and time-frequency analysis of EEG/MEG signals (lecture S. Baillet)
15:15-15:45	Time-frequency analysis Time-frequency representation of EEG/MEG signals
15:45-16:15	Beyond the GUI Plugins in Brainstorm Scripting Collaboration and GitHub
16:15-16:30	Wrap-up

Day 2

09:00-09:45	Foundations of source estimation (Lecture S. Baillet)
09:45-12:00	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
12:00-13:00	Lunch
13:00-14:05	Subject level analysis Subject averages (sensor and source levels) Within subject differences
14:05-15:00	Group level analysis Preparing sensor and source data Grand averages
15:00-15:45	Connectivity (Lecture S. Baillet)
15:45-16:15	Connectivity Connectivity scout level
16:15-16:30	Wrap-up

We provide 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 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.

Note: The event is now at full capacity. As such the registration is closed. Thank you for your interest. Keep posted for new workshop announcements.

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-<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/XXXXX|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXX|Lectures slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXX|Walkthrough]] | [[https://forms.gle/XXXXX|Survey]]<<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://mcgill-my.sharepoint.com/:b:/g/personal/raymundo_cassanigonzalez_mcgill_ca/EWRe_AHXegNOgHFQlXxS2xgBXmDp3eD3KoJDycWEI1TsHA?e=1AvkGn|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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{{{#!wiki comment 

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]].
+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]].
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-. 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:
+. 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:
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-  * '''`ds000117-iitbombay`''': Dataset used during the workshop session

}}}

{{{#!wiki comment
+  * '''`ds000117_S1R1`''': Dataset 1 used during the workshop session
  * '''`UQTR_S1S2_R1R2`''': Dataset 2 used during the workshop session
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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>)>>08:30-09:00<<HTML(</TD><TD>)>>'''Onsite assistance in installing the material for the training session'''<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>09:45-10:30<<HTML(</TD><TD>)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<<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>)>>
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-<<HTML(<TR><TD>)>>10:30-12:30<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''
+<<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'''
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+Frequency filters
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-<<HTML(<TR><TD>)>>12:30-14:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>14:00-16:00<<HTML(</TD><TD>)>>'''Pre-processing and poching'''

Frequency filters
+<<HTML(<TR><TD>)>>13:00-16:00<<HTML(</TD><TD>)>>'''Pre-processing and epoching'''
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+Statistics, sensor level
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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>)>>14:45-15:15<<HTML(</TD><TD>)>> Spectral and '''time-frequency analysis of EEG/MEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>16:45-17:15<<HTML(</TD><TD>)>>'''Time-frequency analysis'''
+<<HTML(<TR><TD>)>>15:15-15:45<<HTML(</TD><TD>)>>'''Time-frequency analysis'''
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-<<HTML(<TR><TD>)>>17:15-17:30<<HTML(</TD><TD>)>>'''Wrap-up'''
+<<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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-<<HTML(<TR><TD>)>>09:45-12:30<<HTML(</TD><TD>)>>'''Sources estimation '''
+<<HTML(<TR><TD>)>>09:45-12:00<<HTML(</TD><TD>)>>'''Sources estimation '''
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+Statistics, source level
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-<<HTML(<TR><TD>)>>12:30-14:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>14:00-16:00<<HTML(</TD><TD>)>>'''Subject level analysis'''
+<<HTML(<TR><TD>)>>13:00-14:05<<HTML(</TD><TD>)>>'''Subject level analysis'''
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-Statistical testing

Subject averages (sensors, time-frequency and sources)
+Subject averages (sensor and source levels)
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-<<HTML(<TR><TD>)>>16:00-17:15<<HTML(</TD><TD>)>>'''Group level analysis'''
+<<HTML(<TR><TD>)>>14:05-15:00<<HTML(</TD><TD>)>>'''Group level analysis'''
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-Preparing sensor, time-frequency and sources data
+Preparing sensor and source data
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-Head modelling, cortical source reconstruction
+Grand averages
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-<<HTML(<TR><TD>)>>17:15-17:30<<HTML(</TD><TD>)>>'''Wrap-up'''
+<<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

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>16:15-16:30<<HTML(</TD><TD>)>>'''Wrap-up'''
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-=== Day 3 ===
<<HTML(<TABLE>)>>

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

Scripting

Plugins

GitHub

<<HTML(</TD></TR>)>>

<<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'''

<<HTML(</TABLE>)>>

}}}

== Program ==
=== Day 1 ===
<<HTML(<TABLE>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Biological origins of EEG/MEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Pre-processing and epoching'''

<<HTML(</TD></TR>)>>

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Foundations of''' '''source estimation '''''(Lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Sources estimation ''' <<HTML(</TD></TR>)>>
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-<<HTML(</TABLE>)>>

=== Day 2 ===
<<HTML(<TABLE>)>>

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

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

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Subject level analysis'''

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Group level analysis'''

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>><<HTML(</TD><TD>)>>'''Participants working with their own data'''<<HTML(</TD></TR>)>>

<<HTML(</TABLE>)>>

We provide [[https://box.bic.mni.mcgill.ca/s/XXXX|a detailed step-by-step walkthrough]] of the data analyses performed during the training.
+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.
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-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. We may ask that you pair with other attendees, for logistics purposes.
+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]].
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-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.
+== Troubleshooting ==
For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )
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-{{{#!wiki comment
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-<<HTML(<FONT color=red>)>>'''Note: '''<<HTML(</FONT>)>>__The event is now at full capacity on the first day__. You may still register but seating priority will be given to the people that already registered.

}}}
 
 . <<EmbedContent(https://neuroimage.usc.edu/bst/workshop.js)>> <<HTML(<div id="bst_table" style=""><FORM METHOD="post" ACTION="https://neuroimage.usc.edu/bst/workshop_reg.php" name="form" onSubmit="return validateForm(this);"><TABLE><TR><TD align=right>First name * </TD> <TD><INPUT type="text" name="firstname" size=40></TD></TR> <TR><TD align=right>Last name * </TD> <TD><INPUT type="text" name="lastname" size=40></TD></TR> <TR><TD align=right>Title / Occupation * </TD> <TD><INPUT type="text" name="title" size=40></TD></TR> <TR><TD align=right>Institution * </TD> <TD><INPUT type="text" name="institution" size=40></TD></TR> <TR><TD align=right>Which days are you planning <BR> on attending (1, 2 or both)? * </TD> <TD><INPUT type="text" name="city" size=40></TD></TR> <TR><TD align=right>Email address * </TD> <TD><INPUT type="text" name="email" size=40></TD></TR> <TR><TD align=right>Phone </TD> <TD><INPUT type="text" name="phone" size=40></TD></TR></TABLE> <BR> <BR> <INPUT type="submit" value="Register now!" style="width:200px">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="WorkshopUQTR2024Reg">View list of registered participants </A> <BR><BR><BR><INPUT type="hidden" name="eventname" value="UQTR2024"> </FORM> </div>)>>
+<<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.

Software

Users

Development