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Little Rock, Arkansas, USA: January 24-26, 2024

Three-day Brainstorm training, MEG- and EEG-oriented.
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

Where	Arkansas Children's Hospital
When	January 24-26, 2024, 9:00-16:30
Registration	Closed
Organizers	Diana Escalona-Vargas (Arkansas Children's Hospital, USA)
Instructors	Sylvain Baillet and Raymundo Cassani (Montreal Neurological Institute / McGill, Canada)
Audience	Users interested in analyzing MEG/EEG recordings using Brainstorm. Some experience with MEG/EEG is recommended. Teaching in English. Participants are required to have an academic affiliation
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, first we will go through the main processing steps using data from one of the participants following the processing pipeline described in the article MEG/EEG Group Analysis With Brainstorm and the corresponding online tutorial. In a second part, we will use pre-processed data from two participants to show the steps for group analysis.

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):
https://box.bic.mni.mcgill.ca/s/AFXWFz4mC7C2l6V
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: Arkansas_S1S2_R1R2.zip (920 MB):
https://box.bic.mni.mcgill.ca/s/goTIK9p0PI98ZBD
Unzip the downloaded file on your desktop: it will create a new folder named Arkansas_S1S2_R1R2. It contains pre-processed data for two participants, two runs ech.
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
- Arkansas_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 MEG and EEG (lecture S. Baillet)
09:30-10:00	Introduction to Brainstorm (lecture R. Cassani)
10:30-11:20	Loading anatomy and recordings Brainstorm database Set anatomy Review RAW recordings Events and event functions
11:20-12:00	Pre-processing Frequency filters Artifact detection Artifact correction with SSP
12:00-13:00	Lunch
13:00-13:45	Pre-processing (cont.) Artifact correction with SSP
13:45-14:30	Epoching and Importing Import epochs and sensor averages Visualization of epochs/trials Average trials
14:30-15:00	Spectral and time-frequency analysis of MEG/EEG signals (lecture S. Baillet)
15:00-15:45	Time-frequency analysis Time-frequency representation of EEG/MEG signals
15:45-16:00	Day 1 wrap-up

Day 2

08:30-09:00	Onsite assistance, materials, concepts, day 1 steps
09:00-09:45	Source modelling (Lecture S. Baillet)
09:45-11:30	Sources estimation Forward model (aka Head model) Noise covariance matrix Source estimation
11:30-12:00	Sources estimation Cortex parcellations: Atlases and Scouts
12:00-13:00	ACRI Visiting Scholars Research Seminar (Lecture S. Baillet) Lunch will be provided
13:00-13:30	Subject level statistics Statistics, sensor space Statistics, source space
13:30-14:00	Sharing Protocols Exporting protocols Importing protocols Load provided protocol: 2 participants, 2 runs each
14:00-15:30	Subject level analysis Subject averages (sensors, sources, and time-frequency) Within subject differences
15:30-16:30	Group level analysis Preparing source subject-averages Co-registration to default anatomy Group averages

Day 3

09:00-09:30	Connectivity & resting-state & evoked response (Lecture S. Baillet)
09:30-10:00	Connectivity Functional connectivity
10:00-11:00	Beyond the GUI Scripting GitHub
11:00-12:00	Participants working with their own data
12:00-13:00	Lunch
12:00-15:30	Participants working with their own data (cont.)
16:15-16:30	Wrap-up

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 MEG/EEG 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 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.

We provide a detailed step-by-step walkthrough of the data analyses performed at the training.

Troubleshooting

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

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-<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>January 24-26, 2023, 9:00-17:00<<HTML(</TD></TR>)>>

<<HTML(<!--<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://redcapwap.archildrens.org/redcap/surveys/?s=WRT4WCC4PH4P9RF3|Please visit this page]]. <<HTML(</TD></TR>-->)>>
+<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>January 24-26, 2024, 9:00-16:30<<HTML(</TD></TR>)>>

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

<<HTML(<!--<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Lectures slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Walkthrough]] | [[https://forms.gle/XXXXXXXX|Survey]]<<HTML(</TD></TR>-->)>>
+<<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing MEG/EEG recordings using Brainstorm.<<BR>>Some experience with MEG/EEG is recommended. Teaching in English.<<BR>>Participants are required to have an academic affiliation <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/H9QmxHuNlr1c1Ld|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/X1CaQHE9JV6BWN9|Lectures slides]] | [[https://box.bic.mni.mcgill.ca/s/vgMLfe30Ky5ZLxn|Walkthrough]] | [[https://forms.gle/b8LtFjp1pN1TZvf4A|Survey]] <<HTML(</TD></TR>)>>
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-TBD
+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, first we will go through the main processing steps using data from one 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]]. In a second part, we will use pre-processed data from two participants to show the steps for group analysis.
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-. Download the tutorial dataset (360 MB):
  . https://box.bic.mni.mcgill.ca/s/XXXXX
 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshop_XXXX`'''
 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://box.bic.mni.mcgill.ca/s/AFXWFz4mC7C2l6V
 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: '''`Arkansas_S1S2_R1R2.zip`''' (920 MB):<<BR>>
 https://box.bic.mni.mcgill.ca/s/goTIK9p0PI98ZBD
 1. Unzip the downloaded file on your desktop: it will create a new folder named `Arkansas_S1S2_R1R2`. It contains pre-processed data for two participants, two runs ech.
 1. Final check: after following the steps above, you should have 4 folders on your desktop:
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-  * '''`workshop_XXXX`''': Dataset used during the workshop session
}}}
+  * '''`ds000117_S1R1`''': Dataset 1 used during the workshop session
  * '''`Arkansas_S1S2_R1R2`''': Dataset 2 used during the workshop session
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-<<HTML(<TR><TD>)>>09:00-10:00<<HTML(</TD><TD>)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:00-11:00<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''
+<<HTML(<TR><TD>)>>09:00-09:30<<HTML(</TD><TD>)>>'''Biological origins of MEG and EEG''' ''(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>)>>10:30-11:20<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''
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-Events

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

<<HTML(<TR><TD>)>>11:00-12:00<<HTML(</TD><TD>)>>'''Pre-processing'''
+Events and event functions

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

<<HTML(<TR><TD>)>>11:20-12:00<<HTML(</TD><TD>)>>'''Pre-processing'''
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-<<HTML(<TR><TD>)>>13:00-14:30<<HTML(</TD><TD>)>>'''Events and epoching'''

Events functions
+<<HTML(<TR><TD>)>>13:00-13:45<<HTML(</TD><TD>)>>'''Pre-processing (cont.)'''

Artifact correction with SSP

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

<<HTML(<TR><TD>)>>13:45-14:30<<HTML(</TD><TD>)>>'''Epoching and Importing'''
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+Visualization of epochs/trials

Average trials
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-<<HTML(<TR><TD>)>>15:00-16:30<<HTML(</TD><TD>)>>'''Time-frequency analysis'''
+<<HTML(<TR><TD>)>>15:00-15:45<<HTML(</TD><TD>)>>'''Time-frequency analysis'''
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+<<HTML(<TR><TD>)>>15:45-16:00<<HTML(</TD><TD>)>>'''Day 1 wrap-up'''

<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>08:30-09:00<<HTML(</TD><TD>)>>'''Source modelling''' ''(Lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:00-10:45<<HTML(</TD><TD>)>>'''Sources estimation '''
+<<HTML(<TR><TD>)>>08:30-09:00<<HTML(</TD><TD>)>> Onsite assistance, materials, concepts, day 1 steps<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:00-09:45<<HTML(</TD><TD>)>>'''Source modelling''' ''(Lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:45-11:30<<HTML(</TD><TD>)>>'''Sources estimation '''
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-Source estimation (surfaces and volume source spaces)
+Source estimation

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

<<HTML(<TR><TD>)>>11:30-12:00<<HTML(</TD><TD>)>>'''Sources estimation '''
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-<<HTML(<TR><TD>)>>10:45-12:00<<HTML(</TD><TD>)>>'''Subject level statistics'''
+<<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>'''ACRI Visiting Scholars Research Seminar''' ''(Lecture S. Baillet)'' <<BR>> Lunch will be provided <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:00-13:30<<HTML(</TD><TD>)>>'''Subject level statistics'''
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-<<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>'''ACRI Visiting Scholars Research Seminar''' ''(Lecture S. Baillet)'' <<BR>> Lunch will be provided <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:00-14:30<<HTML(</TD><TD>)>>'''Subject level analysis'''

Subject averages (sensors, time-frequency and sources)
+<<HTML(<TR><TD>)>>13:30-14:00<<HTML(</TD><TD>)>>'''Sharing Protocols'''

Exporting protocols

Importing protocols

Load provided protocol: 2 participants, 2 runs each

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

<<HTML(<TR><TD>)>>14:00-15:30<<HTML(</TD><TD>)>>'''Subject level analysis'''

Subject averages (sensors, sources, and time-frequency)
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-<<HTML(<TR><TD>)>>14:30-16:00<<HTML(</TD><TD>)>>'''Group level analysis'''

Preparing sensor, time-frequency and sources data
+<<HTML(<TR><TD>)>>15:30-16:30<<HTML(</TD><TD>)>>'''Group level analysis'''

Preparing source subject-averages

Co-registration to default anatomy

Group averages
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-<<HTML(<TR><TD>)>>12:00-15:30<<HTML(</TD><TD>)>>'''Participants working with their own data'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:30-16:00<<HTML(</TD><TD>)>>'''Wrap-up'''
+<<HTML(<TR><TD>)>>12:00-15:30<<HTML(</TD><TD>)>>'''Participants working with their own data (cont.)'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>16:15-16:30<<HTML(</TD><TD>)>>'''Wrap-up'''
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-{{{#!wiki comment

We provide [[https://box.bic.mni.mcgill.ca/s/XXXX|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]].
}}}
+We provide [[https://box.bic.mni.mcgill.ca/s/vgMLfe30Ky5ZLxn|a detailed step-by-step walkthrough]] of the data analyses performed at the training.

Software

Users

Development