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| The hands-on part of this workshop 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]]. | 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. |
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| <<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>)>>'''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>)>> |
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| <<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[TBD|Slides]] | [[TBD|Walkthrough]] | [[TBD|Survey]]<<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/Z1ZWryzcTTaC79e|Walkthrough]] | [[https://forms.gle/sWNCLJ42Q9NtgkFNA|Survey]]<<HTML(</TD></TR>)>> |
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| 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. If you encounter any trouble at setting Brainstorm please show up 30 min before the start of the workshop. |
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. |
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| Please read carefully the following instructions on:<<BR>>[[WorkshopGeneralInstall|preparing your laptop for the training]] | 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]] |
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| TODO The workshop dataset is a pre-processed version of the dataset in used in the [[Tutorials/CorticomuscularCoherence|Brainstorm tutorial on corticomuscular coherence]]. It consists of simultaneous MEG and EMG (left arm) recordings during prompted left arm movements. A full description of the dataset can be found [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence#Dataset_description|here]]. |
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 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 |
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| === Day 1 === | |
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| <<HTML(<TR><TD>)>>10:00-10:30<<HTML(</TD><TD>)>>Introduction to Brainstorm (lecture)<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>09:00-09:45<<HTML(</TD><TD>)>>'''Biological origins of EEG/MEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>10:30-11:20<<HTML(</TD><TD>)>>'''Loading anatomy and recordings''' | <<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''' |
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| Import events | Manage events |
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| <<HTML(<TR><TD>)>>11:20-12:30<<HTML(</TD><TD>)>>'''Pre-processing''' | <<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 poching''' |
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| Artifact correction with SSP <<HTML(</TD></TR>)>> | Artifact correction with ICA and SSP |
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| <<HTML(<TR><TD>)>>12:30-13:15<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>> | Import epochs and sensor averages |
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| <<HTML(<TR><TD>)>>13:15-14:00<<HTML(</TD><TD>)>>'''Analysis''' | <<HTML(</TD></TR>)>> |
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| Coherence (sensor level) | <<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 <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>17:15-17:30<<HTML(</TD><TD>)>>'''Wrap-up''' <<HTML(</TABLE>)>> === Day 2 === <<HTML(<TABLE>)>> <<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 <<HTML(</TD></TR>)>> <<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 analy''' Statistical testing Subject averages (sensors, time-frequency and sources) Within subject differences <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>16:00-17:15<<HTML(</TD><TD>)>>'''Analysis Group level''' Preparing sensor, time-frequency and sources data |
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| Coherence (source level) <<HTML(</TD></TR>)>> | <<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. | === Day 3 === <<HTML(<TABLE>)>> |
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| == Program == === 1. Wednesday am: From raw to ERP === * Introduction to Brainstorm (lecture) * Review the MEG+EEG recordings * Read and organize events * Frequency filters * Artifacts detection and cleaning |
<<HTML(<TR><TD>)>>09:00-10:00<<HTML(</TD><TD>)>>'''Beyond the GUI''' Report viewer |
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| === 2. Tuesday pm: Sensor level analysis === * Epoching and averaging * Time-frequency analysis |
Scripting |
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| === 3. Wednesday am: Creating head and source models === * Import anatomy * Registration MRI-sensors * Forward model * Simulations |
Plugins |
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| === 4. Wednesday pm: Single and distributed sources === * MEG noise covariance: From empty room recordings * EEG noise covariance: From pre-stimulus baselines * Distributed sources / minimum norm estimation * Regions of interest * LCMV Beamformer * Dipole scanning / Volume source models |
GitHub |
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| === 5. Thursday am: Group-level analysis === * Project source maps on MNI template * Statistical testing * Export data to other programs (FieldTrip, SPM, ...) * Scripting * Example for this workshop: https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_practicalmeeg.m |
<<HTML(</TD></TR>)>> |
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| === 6. Thursday pm: User requests === * Bring your own data or prepare your questions |
<<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>)>> We provide [[https://box.bic.mni.mcgill.ca/s/9BXiGy7WpKhgnxu|a detailed step-by-step walkthrough]] of the data analyses performed during the training. |
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| The last session will be mostly dedicated to addressing participants' requests. We encourage you to prepare some EEG/MEG/ECoG/sEEG data you would be interested in processing with Brainstorm. If you are coming with colleagues, try to organize small groups with similar interests (1-4 people). | 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. |
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| The list of file formats that can be read by Brainstorm is available 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. NOTE ON, IF THERE IS NOT DATA ON YOUR OWN, YOU CAN TRY WITH DATA AVAILABLE AT 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]]. 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. |
Mumbai, India June 28-30, 2023
Practical workshop on EEG/MEG analysis at IIT Bombay.
Three-day Brainstorm training, EEG- and MEG-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 | IIT Bombay |
| When | Wednesday, June 28 - Friday 30, 2023 2023: 09:00-17:30 |
| Instructors | Sylvain Baillet and Raymundo Cassani (Montreal Neurological Institute / McGill, Canada) |
| Audience | Users interested in analyzing MEG/EEG/sEEG recordings using Brainstorm. Some experience with MEG/EEG is recommended. Teaching in English. Number of participants: 30 |
| Slides | Intro 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. 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:
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 the processing pipeline 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 (5 GB):
- Unzip the downloaded file on your desktop
- 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
| 09:00-09:45 | Biological origins of EEG/MEG signals (lecture S. Baillet) |
| 09:45-10:30 | Introduction to Brainstorm (lecture R. Cassani) |
| 10:30-12:30 | Loading anatomy and recordings Set anatomy Review RAW recordings Manage events |
| 12:30-14:00 | Lunch |
| 14:00-16:00 | Pre-processing and poching Frequency filters Artifact detection Artifact correction with ICA and SSP Import epochs and sensor averages |
| 16:00-16:45 | Spectral and time-frequency analysis of EEG/MEG signals (lecture S. Baillet) |
| 16:45-17:15 | Time-frequency analysis Time-frequency representation of EEG/MEG signals |
| 17:15-17:30 | Wrap-up |
Day 2
| 09:00-09:45 | Foundations of source estimation (Lecture S. Baillet) |
| 09:45-12:30 | Sources estimation Forward model (aka Head model) Noise covariance matrix Source estimation (surfaces and volume source spaces) Cortex parcellations: Atlases and Scouts |
| 12:30-14:00 | Lunch |
| 14:00-16:00 | Subject level analy Statistical testing Subject averages (sensors, time-frequency and sources) Within subject differences |
| 16:00-17:15 | Analysis Group level Preparing sensor, time-frequency and sources data Head modelling, cortical source reconstruction |
| 17:15-17:30 | Wrap-up |
Day 3
| 09:00-10:00 | Beyond the GUI Report viewer Scripting Plugins GitHub |
| 09:00-12:30 | Participants working with their own data |
| 12:30-14:00 | Lunch |
| 14:00-17:15 | Participants working with their own data |
| 17:15-17:30 | Wrap-up |
We provide 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 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.