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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>)>>'''Where'''<<HTML(</TD><TD>)>>[[http://practicalmeeg2019.org/venue/|ICM]]<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>>[[https://www.iitb.ac.in/|IIT Bombay]] <<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Tuesday Dec 3rd - Thursday Dec 5, 2019: 8:30-17:30<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Wednesday, June 28 - Friday 30, 2023 2023: 09:00-17:30<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Instructors'''<<HTML(</TD><TD>)>>[[AboutUs/FrancoisTadel|Francois Tadel]] (Grenoble Institute of Neuroscience)<<BR>>[[http://www.neurotrack.fr/contact/|Anne-Sophie Dubarry]] (Aix-Marseille University)<<BR>>[[https://cognition.ens.fr/fr/member/8648/aurelien-weiss|Aurélien Weiss]] (ENS)<<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>)>> |
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| <<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing sEEG/EEG/ECoG/MEG recordings using Brainstorm.<<BR>>Teaching in English. <<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>)>>'''Documents'''<<HTML(</TD><TD>)>>[[https://neuroimage.usc.edu/resources/practicalmeeg2019_brainstorm.pdf|Introduction slides]] | [[http://neuroimage.usc.edu/resources/practicalmeeg2019_brainstorm_walkthrough.pdf|Hands-on walkthrough]] | [[https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_practicalmeeg.m|Processing script]] | [[http://neuroimage.usc.edu/resources/practicalmeeg2019_anatomy_soft.pdf|Anatomy processing]]<<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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| The participants are required to <<HTML(<FONT color=red>)>> '''bring a laptop''' <<HTML(</FONT>)>> (an external mouse will add to your comfort). In order to make the session as efficient as possible, we ask all the attendees to <<HTML(<FONT color=red>)>>'''download, install and test'''<<HTML(</FONT>)>> the software and sample dataset on their laptops prior to 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 installation instructions: <<BR>>[[https://neuroimage.usc.edu/brainstorm/WorkshopParis2019#Installation_instructions|How to prepare your laptop for the training]] | == 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:<<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 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: 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: * '''`brainstorm3`''': the software folder, containing the source code and the compiled executable * '''`brainstorm_db`''': your Brainstorm database (which should be empty for now) * '''`ds000117-iitbombay`''': Dataset used during the workshop session |
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| === 1. Tuesday am: From raw to ERP === * Introduction to Brainstorm (lecture) * Review the MEG+EEG recordings * Read and organize events * Frequency filters * Artifacts detection and cleaning |
=== Day 1 === <<HTML(<TABLE>)>> |
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| === 2. Tuesday pm: Sensor level analysis === * Epoching and averaging * Time-frequency analysis |
<<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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| === 3. Wednesday am: Creating head and source models === * Import anatomy * Registration MRI-sensors * Forward model * Simulations |
<<HTML(<TR><TD>)>>09:45-10:30<<HTML(</TD><TD>)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<<HTML(</TD></TR>)>> |
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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 |
<<HTML(<TR><TD>)>>10:30-12:30<<HTML(</TD><TD>)>>'''Loading anatomy and recordings''' |
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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 |
Set anatomy |
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| === 6. Thursday pm: User requests === * Bring your own data or prepare your questions |
Review RAW recordings |
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| == Installation instructions == Before coming to the workshop, you need to download the software and the tutorial dataset (1.6 Gb). To streamline troubleshooting during the session, please save all the downloaded files '''__on your Desktop__'''. |
Manage events |
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| 1. From the Brainstorm [[http://neuroimage.usc.edu/bst/download.php|Download]] page, log in or create a Brainstorm account 1. Download <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>> (75 Mb) 1. If you already have Brainstorm: update it. We need a version released '''after November 18th''' 1. Download the tutorial dataset (1.5 Gb):<<BR>>https://owncloud.icm-institute.org/index.php/s/cNu5jmiOhe7Yuoz/download 1. Unzip the two downloaded files on your desktop 1. Delete the two downloaded zip files 1. Create a folder "'''brainstorm_db'''" 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-practical''': Example dataset used during the training session 1. Start Brainstorm (see following section) 1. Select the menu '''Help > Workshop preparation'''. 1. Follow the instructions: when you see the 3D figure, make sure you see both a transparent head surface and a brain surface. Try to rotate the view with your mouse, and zoom in and out with the mouse wheel. <<BR>><<BR>> {{attachment:test_bst.gif}} 1. If you want to call FieldTrip functions from Brainstorm (multitaper, cluster-based statistics and dipole fitting), '''download and install FieldTrip''' on your computer:<<BR>>http://www.fieldtriptoolbox.org/download/ |
<<HTML(</TD></TR>)>> |
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| == Running Brainstorm for the first time == ==== With Matlab ==== 1. Matlab versions >= 2014b are faster and produce nicer graphics: consider upgrading if possible 1. Start Matlab 1. Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be done automatically 1. Go to the brainstorm3 folder 1. Type "brainstorm" in the command window 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created |
<<HTML(<TR><TD>)>>12:30-14:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>> |
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| ==== Without Matlab ==== 1. The instructions below are valid for the following operating systems: * '''Windows''': Any version ([[https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/SystemRequirements-Release2015b_Windows.pdf|details]]) * '''Linux''': Ubuntu 14.04+, RedHat 6.x+, Debian 7.x, SUSE 11.3+ ([[https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/SystemRequirements-Release2015b_Linux.pdf|details]]) * '''MacOS''': 10.9.5 (Mavericks), 10.10 (Yosemite) ([[https://www.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/SystemRequirements-Release2015b_Macintosh.pdf|details]]) * If your system is not listed, try another version: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]], [[InstallationR2016a|2016a]], [[InstallationR2016b|2016b]], [[InstallationR2017a|2017a]] 1. Download the '''MCR R2015b (9.0)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]] 1. Install the MCR: * __Windows__: Double-click on the .exe and follow the instructions * __MacOS__: Click on the zip file to unzip it, then click on "InstallForMacOSX" * __Linux__: From a terminal, unzip .zip, then run ./install 1. Run the program in brainstorm3/bin/R2015b/ * __Windows__: Double-click on ''brainstorm3.bat'' * __MacOS__: Double-click on ''brainstorm3.command ''and wait for instructions * __Linux__: From a terminal, run:<<BR>>''cd brainstorm3/bin/R2015b/''<<BR>>''./brainstorm3.command '' 1. Troubleshooting for MacOS or Linux: * On recent versions of MacOS, you may get an error message "Application can't be opened because it is from an unidentified developer". This message would appear for all the programs that were not downloaded from the Apple app-store. To go around this verification: right-click on the application > Open, then click on the Open button. * From a terminal, make sure that the file "''brainstorm3.command''" is executable:<<BR>>''chmod a+x brainstorm3.command'' * If nothing happens, run: <<BR>>''./brainstorm3.command MCR_DIR''<<BR>>MCR_DIR is the MCR 9.0 folder (ex: /Applications/MATLAB/MCR/v90) * Try with another binary release: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]], [[InstallationR2016a|2016a]], [[InstallationR2016b|2016b]], [[InstallationR2017a|2017a]]... 1. Troubleshooting for Windows: * Your current user may not have the necessary privileges. If you are an administrator for your computer, you can do the following: right-click on ''brainstorm3.bat'' > Run as administrator. * If you are not the administrator of your computer and Matlab or the MCR are not installed in the standard paths, Brainstorm may have trouble finding them. To specify manually the path of the MCR or Matlab folder, right-click on ''brainstorm3.bat'' > Edit. Fill the second line of the script (Example: @SET MATLABROOT="C:\Program Files\MATLAB\R2015b"), save the file, and try to execute it again. 1. On Linux or MacOS, you may be asked to select the folder where you installed the MCR. 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created. |
<<HTML(<TR><TD>)>>14:00-16:00<<HTML(</TD><TD>)>>'''Pre-processing and poching''' Frequency filters Artifact detection Artifact correction with ICA and SSP Import epochs and sensor averages <<HTML(</TD></TR>)>> <<HTML(</TD></TR>)>> <<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 analysis''' 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>)>>'''Group level analysis''' Preparing sensor, time-frequency and sources data Head modelling, cortical source reconstruction <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>17:15-17:30<<HTML(</TD><TD>)>>'''Wrap-up''' <<HTML(</TABLE>)>> === 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>)>> 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: it will create a new folder named ds000117-iitbombay.
- Final check: after following the steps above, you should have 3 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-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 analysis Statistical testing Subject averages (sensors, time-frequency and sources) Within subject differences |
| 16:00-17:15 | Group level analysis 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.