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* Default anatomy | * Default anatomy |
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'''Q&A''' |
'''Q&A session''' |
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Before coming to the workshop, you need to download the software and the tutorial dataset from the Brainstorm website (110Mb). Additionally, the epileptogenicity analysis is based on SPM12 (100Mb). To streamline troubleshooting 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 (330Mb). To streamline troubleshooting during the session, please save all the downloaded files '''__on your Desktop__'''. |
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* '''Brainstorm software''': <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>> (70 Mb) * '''Tutorial dataset''': <<HTML(<FONT color=red>)>>workshop_cuttingeeg.zip<<HTML(</FONT>)>> (41 Mb) 1. If you already have Brainstorm on your laptop, make sure to update it before coming. 1. Download SPM12 from the UCL website, free registration required:<<BR>>http://www.fil.ion.ucl.ac.uk/spm/software/download/ 1. Unzip the three downloaded files on your desktop, then delete them 1. Create a folder "'''brainstorm_db'''" on your '''Desktop ''' 1. Final check: you should have now 4 folders on your desktop: |
* '''Brainstorm software''': <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>> (60 Mb) * '''Tutorial dataset''': <<HTML(<FONT color=red>)>>sample_introduction.zip<<HTML(</FONT>)>> (330 Mb) 1. If you already have Brainstorm, make sure that the version was released <<HTML(<FONT color=red>)>>'''after May 1st'''<<HTML(</FONT>)>>. 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 now 3 folders on your desktop: |
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* '''workshop_cuttingeeg''': Example dataset used during the training session * '''spm12''': SPM toolbox, required for the epileptogenicity analysis 1. Run Brainstorm, make sure it works correctly on your computer (read the next section) 1. Tell Brainstorm where you unzipped SPM12: Menu File > Edit preferences > SPM toolbox. |
* '''sample_introduction''': Example dataset used during the training session 1. Run Brainstorm, to make sure it works correctly on your computer (read the following section) |
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1. Tell Brainstorm where you unzipped SPM12: Menu File > Edit preferences > SPM toolbox. <<BR>>No need to add SPM to the Matlab path either, Brainstorm will do it when needed. | |
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. The Brainstorm distribution includes a stand-alone version, created with the Matlab Compiler, which can be used without any Matlab license. However, compiled code cannot execute Matlab scripts that are not compiled, which prevents the use of external toolboxes (SPM, FieldTrip).<<BR>><<BR>>The last part of this hands-on session will rely on functions from the SPM toolbox, therefore if you use the compiled version, you wouldn't be able to follow the session until the end on your laptop. If you still want to run the compiled version of Brainstorm on your laptop, please refer to the main [[https://neuroimage.usc.edu/brainstorm/Installation|installation page]]. | 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 here, try with another version: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]], [[http://InstallationR2016a|2016a]], ... 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]], ... 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. |
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{{attachment:test_bst.gif}} | {{http://neuroimage.usc.edu/brainstorm/WorkshopToronto2015Install?action=AttachFile&do=get&target=test_bst.gif|test_bst.gif|class="attachment"}} |
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For any technical problem, please contact Raymundo Cassani (raymundo.cassani@mcgill.ca) | For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca ) |
Live Brainstorm workshop and Q&A, Online: May XX, 2021
Two-hour online Brainstorm workshop and Q&A, live on Zoom.
General information
Where | Zoom (link will provided after registration) |
When | *day May XX, 2021: XX:XX-XX:XX EDT |
Instructors | Sylvain Baillet (Montreal Neurological Institute / McGill, Canada) Raymundo Cassani (Montreal Neurological Institute / McGill, Canada) |
Audience | Open to both beginners and advanced users. Bring your own questions. |
Program
This workshop is based on topics presented at detail in the get started tutorials.
Brainstorm overview
- Main user interface
- Software structure
- Typical data workflow
Anatomy data
- Database explorer
- MRI volumes and surfaces
- Default anatomy
Functional data
- Database explorer
- Reviewing recordings
- Visualization of recordings, montages and options
- Events and artifact removal with SSP
- Importing event-related data
- Forward model (head model)
- Inverse problem (source estimation) and normalization
- Visualization of sources, scouts and options
Process tab
- Process1 and Process2
- Overview of process categories
- Pipeline editor
- Process options and online help
- Pipeline as script
Q&A session