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| = Brainstorm Training Workshop at UQAM = | = MEG / Brainstorm Workshop (UQAM summer school) = |
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| * '''When''': Saturday, April 28, 2012 (9am - 5pm)''' ''' * '''Where: '''MIT [[http://whereis.mit.edu/?go=32|Building 32]] (Stata Center) Room 141 |
* '''When''': Wednesday, July 11, 2012 (9am - 6pm)''' ''' * '''Where: '''UdeM, room D-427 of the [[http://www.umontreal.ca/plancampus/pavillons/pav03.html|Marie-Victorin Building located at 90 Vincent d'Indy Street]], right next to the metro station "Edouard-Montpetit". == Program == '''Morning: Introduction to Magnetoencephalography''' * 9h00 : Welcome & Introduction (Pierre Jolicoeur, UdeM) * 9h15 - 10h00 : Principles of MEG: practical aspects in data collection and experimental set-ups (Elizabeth Bock, !McGill) * 10h00 - 11h00 : MEG signal extraction and source imaging crash-course: concepts & methodology (Esther Florin, !McGill) * 11h00 - 11h15 : Coffee break * 11h15 - 12h15 : MEG applied to cognitive neuroscience (Pierre Jolicoeur, UdeM) * 12h15 - 13h30 : Lunch break '''Afternoon: Brainstorm hands-on session''' * 13h30 - 14h00 : Introduction to Brainstorm (Francois Tadel, !McGill) * 14h00 - 15h30 : Database explorer, reviewing continuous recordings, artifact correction, filtering and epoching, averaging, observation of a typical somato-sensory evoked response * 15h30 - 15h45 : Coffee break * 15h45 - 17h00 : Head modeling, cortical source reconstruction, definition of ROIs, tracking the processing of the sensory information millisecond by millisecond at the cortex level * 17h00 - 18h00 : Introduction to advanced features, depending on the audience specific requests: Frequency and time-frequency analysis, group analysis, anatomical atlases, advanced scripting interface, ... |
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| * Bring your own laptop (any operating system, with or without Matlab installed) with Brainstorm installed (version of '''April 20th''' or later), and the sample dataset (see instructions below). | * Bring your own laptop: * Any operating system, with or without Matlab installed, * Relatively recent hardware (some of the tutorial steps require a lot of computation power and could be too long on older laptops), * '''Brainstorm must be installed''' (version of '''July 2nd''' or later, see instructions below), * The '''sample dataset must be downloaded''' (see instructions below) * Make sure you have at least '''10Gb of free space''' on your hard drive |
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| * Participants encountering issues with the installation process are encouraged to visit the ''laptop clinics'' that will be held prior to the Brainstorm training session: * '''April 27 / all day''': MIT Bldg 46 Atrium (3rd floor) during the MEG symposium, * '''April 28 @ 8am''': MIT Bldg 32, outside room 141, * Until then, [[mailto:brainstorm@sipi.usc.edu|email us]] with your questions. |
* Participants who do not follow the instruction on this page before the workshop will not be able to follow the afternoon hands-on session |
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| Before coming to the workshop, you need to download the software and the tutorial dataset from the Brainstorm website (approximately 400Mb). It requires a free registration for demographics purposes. To streamline troubleshooting and instructions during the session, please save all the downloaded files '''__on your Desktop__'''. | Before coming to the workshop, you need to download the software and the tutorial dataset from the Brainstorm website (300 to 650Mb). It requires a free registration for demographics purposes. To streamline troubleshooting and instructions during the session, please save all the downloaded files '''__on your Desktop__'''. |
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| 1. From the Brainstorm [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] page, login or create a Brainstorm account (registration is free) | 1. From the Brainstorm [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] page, log in or create a Brainstorm account (registration is free) |
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| * '''Tutorial dataset''': sample_workshop.zip (240 Mb) * '''Matlab Component Runtime (MCR)''': ONLY if you do not have Matlab installed (300 Mb) 1. Note: if you already have Brainstorm installed, make sure that the version was released''' after April 18th'''. |
* '''Tutorial dataset''': sample_workshop_uqam.zip (260 Mb) * '''Matlab Component Runtime (MCR)''': ONLY if you do __not__ have Matlab installed (350 Mb) 1. Note: if you already have Brainstorm installed, make sure that the version was released''' after July 2nd'''. |
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| 1. If you are using the stand-alone version (without Matlab), install the MCR library: | 1. If you are using the stand-alone version (__without__ Matlab), install the MCR library: |
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| * '''sample_workshop''': Example dataset to be used during the training session | * '''sample_workshop_uqam''': Example dataset to be used during the training session 1. Now run Brainstorm, to make sure it starts fine (read carefully the following section) |
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| In order to make sure that Brainstorm works properly, and to get more familiar with the software, we recommend that you follow at least the first half of the the [[Tutorials|online tutorials]]: | In order to make sure that Brainstorm works properly, and to get more familiar with the software, we recommend that you read and follow at least the first three online tutorials: |
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| * [[Tutorials/TutImportRecordings|3. Importing MEG recordings]] * [[Tutorials/TutExploreRecodings|4. Exploring the recordings]] |
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| * Sylvain Baillet | |
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For those who need help prior to the meeting, please come to our laptop clinics: * '''April 27 / all day''': MIT Bldg 46 Atrium (3rd floor) during the !McGovern Institute Annual Symposium * '''April 28 @ 8am''': MIT Bldg 32, outside room 141 |
MEG / Brainstorm Workshop (UQAM summer school)
General information
When: Wednesday, July 11, 2012 (9am - 6pm)
Where: UdeM, room D-427 of the Marie-Victorin Building located at 90 Vincent d'Indy Street, right next to the metro station "Edouard-Montpetit".
Program
Morning: Introduction to Magnetoencephalography
9h00 : Welcome & Introduction (Pierre Jolicoeur, UdeM)
9h15 - 10h00 : Principles of MEG: practical aspects in data collection and experimental set-ups (Elizabeth Bock, McGill)
10h00 - 11h00 : MEG signal extraction and source imaging crash-course: concepts & methodology (Esther Florin, McGill)
- 11h00 - 11h15 : Coffee break
- 11h15 - 12h15 : MEG applied to cognitive neuroscience (Pierre Jolicoeur, UdeM)
- 12h15 - 13h30 : Lunch break
Afternoon: Brainstorm hands-on session
13h30 - 14h00 : Introduction to Brainstorm (Francois Tadel, McGill)
- 14h00 - 15h30 : Database explorer, reviewing continuous recordings, artifact correction, filtering and epoching, averaging, observation of a typical somato-sensory evoked response
- 15h30 - 15h45 : Coffee break
- 15h45 - 17h00 : Head modeling, cortical source reconstruction, definition of ROIs, tracking the processing of the sensory information millisecond by millisecond at the cortex level
- 17h00 - 18h00 : Introduction to advanced features, depending on the audience specific requests: Frequency and time-frequency analysis, group analysis, anatomical atlases, advanced scripting interface, ...
Requirements
The workshop
- Bring your own laptop:
- Any operating system, with or without Matlab installed,
- Relatively recent hardware (some of the tutorial steps require a lot of computation power and could be too long on older laptops),
Brainstorm must be installed (version of July 2nd or later, see instructions below),
The sample dataset must be downloaded (see instructions below)
Make sure you have at least 10Gb of free space on your hard drive
- Power plugs will be available at each desk.
- Participants who do not follow the instruction on this page before the workshop will not be able to follow the afternoon hands-on session
The software
Brainstorm is available in two distinct forms, both available for Windows, Linux and MacOSX:
- An open-source Matlab application (Matlab required)
Necessary: Matlab version R2006a (7.2), or later
- Optional: Signal Processing Toolbox (for frequency filtering and resampling)
- A stand-alone Java executable (Matlab not required)
- Requires the free download of the Matlab runtime library
To check if your operating system is supported: visit this page
Installation instructions
Before coming to the workshop, you need to download the software and the tutorial dataset from the Brainstorm website (300 to 650Mb). It requires a free registration for demographics purposes. To streamline troubleshooting and instructions during the session, please save all the downloaded files on your Desktop.
From the Brainstorm Download page, log in or create a Brainstorm account (registration is free)
You will then be able to download the following files to your Desktop folder:
Brainstorm software: brainstorm_YYMMDD.zip (45 Mb)
Tutorial dataset: sample_workshop_uqam.zip (260 Mb)
Matlab Component Runtime (MCR): ONLY if you do not have Matlab installed (350 Mb)
Note: if you already have Brainstorm installed, make sure that the version was released after July 2nd.
- Unzip all the zip files
If you are using the stand-alone version (without Matlab), install the MCR library:
Windows: Double-click on the .exe and follow the instructions
Linux: From a terminal, unzip .zip, then run ./install
MacOS: Click on the zip file to unzip it, then click on "InstallForMacOSX"
- Delete the zip files / the installation files
Create a folder "brainstorm_db" on your Desktop folder
- Final check: you should have now 3 folders on your Desktop:
brainstorm3: Program folder, with the Matlab source code and the compiled executable
brainstorm_db: Folder for the Brainstorm database (empty)
sample_workshop_uqam: Example dataset to be used during the training session
- Now run Brainstorm, to make sure it starts fine (read carefully the following section)
Running Brainstorm for the first time
With Matlab
- Start Matlab
DO NOT add the brainstorm3 folder to your path: Brainstorm will take care of that,
Go to the brainstorm3 folder from the Matlab command window,
Type "brainstorm" in the Matlab command window and press enter,
- When asked for the location of the Brainstorm database folder, pick the folder "brainstorm_db" you have just created on the Desktop.
Without Matlab
Run the executable file located in brainstorm3/bin/R2012a/
Windows: Double-click on brainstorm3.bat
Linux: From a terminal, cd brainstorm3/bin/R2012a/
Make sure that the file brainstorm.command is executable:
=> chmod a+x brainstorm.commandrun ./brainstorm.command
MacOS: Double-click on brainstorm.command
- When you start Brainstorm for the first time on Linux or MacOS, you will be prompted to select the folder where you installed the MCR
When asked for the location of the Brainstorm database folder, pick the folder brainstorm_db on your Desktop.
Getting ready for the workshop
In order to make sure that Brainstorm works properly, and to get more familiar with the software, we recommend that you read and follow at least the first three online tutorials:
The slides presented during the workshop are available here:
Troubleshooting
For any technical problem, please contact Francois Tadel ( francois.tadel@mcgill.ca )