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| = Prepare your laptop for the workshop = == Important notes == * Working with MEG/EEG/SEEG recordings involves a lot of computational resources and large display windows. Therefore we recommend that you bring a laptop with a decent processing capacity, '''4Gb RAM''', a '''64bit''' operating system, and a '''screen larger than 13"'''. |
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| * You would add to your comfort by bringing an '''external mouse'''. Most of the manipulations are done with the mouse, and some involve an intensive use of the mouse wheel/scrolling. | == Requirements == In order to make the workshop as efficient as possible, we ask all the attendees to prepare their laptops by: |
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| * Don't forget your '''power adapter'''! | 1. '''Installing''' and '''testing''' Brainstorm in your laptop, and 2. '''Downloading''' the workshop dataset prior to the workshop. |
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| == Installation instructions == Before coming to the workshop, you need to download the software and the tutorial dataset from the Brainstorm website (200Mb). To streamline troubleshooting during the session, please save all the downloaded files '''__on your Desktop__'''. |
== 1. Install Brainstorm == Please read carefully the following instructions to <<HTML(<FONT color=red>)>>'''download'''<<HTML(</FONT>)>>, <<HTML(<FONT color=red>)>>'''install'''<<HTML(</FONT>)>> and <<HTML(<FONT color=red>)>>'''test'''<<HTML(</FONT>)>> Brainstorm: <<BR>>[[WorkshopGeneralInstall|Preparing your laptop for the training]] |
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| 1. Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page, complete the quick and free registration process. 1. If you don't receive the confirmation email, please check your '''spam folder'''. 1. Download the following files to '''your Desktop''' '''folder''': * '''Brainstorm software''': <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>> (source+binary, 90 Mb) * '''Tutorial dataset''': <<HTML(<FONT color=red>)>>workshop_cuttingeeg.zip<<HTML(</FONT>)>> (162 Mb) 1. If you already have Brainstorm on your laptop, make sure to update it before coming. 1. Unzip the two downloaded files on your desktop, then delete them 1. Create a folder "'''brainstorm_db'''" on your '''Desktop ''' 1. Final check: you should have now 3 folders on your desktop: * '''brainstorm3''': Program folder, with the source code and the compiled executable * '''brainstorm_db''': Brainstorm database (empty) * '''workshop_cuttingeeg''': Example dataset used during the training session 1. Run Brainstorm, make sure it works correctly on your computer (see next sections) == Running Brainstorm for the first time == If you don't have a Matlab license, you can get a temporary one for the duration of the conference: https://cuttingeeg2021.lpl-aix.fr/t/matlab-installation-licenses-available/151 ==== With Matlab (2014b minimum) ==== 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 database folder, pick the "brainstorm_db" you have just created 1. '''Install SPM12''': Menu Plugins > spm12 > Install. ==== Without Matlab ==== 1. Install the Matlab Runtime '''R2020a (9.8)''': [[https://www.mathworks.com/products/compiler/matlab-runtime.html|Mathworks website]] 1. Run the program in brainstorm3/bin/R2020a/ * 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/R2020a/<<BR>>'' ''./brainstorm3.command '' 1. For troubleshooting, see the [[https://neuroimage.usc.edu/brainstorm/Installation#Start_Brainstorm|Installation]] page. == Make sure it works == To make sure Brainstorm works properly or your computer: * Select the menu: '''Help > Workshop preparation'''. * 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 or two-finger pad scroll. <<BR>><<BR>> {{attachment:bst_test_2021.png}} |
== 2. Workshop dataset == TBD. |
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| For any technical problem, please contact Francois Tadel ( francois.tadel@mcgill.ca ) | For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca ) |
Los Angeles, CA, USA: October 18th, 2023
Half-day workshop, as part of the CuttingGrden2023 conference. This session will be an introduction to Brainstorm for EEG analysis. Participants will learn how to use Brainstorm and acces its new tools on their personal laptops.
General information
| Where | Univerisyt of Southern California |
| When | Wednesday October 18th, 2023: 13:00-17:30 |
| Instructor | Raymundo Cassani & Takfarinas Medani |
| Registration | Please visit this page. |
| Audience | Users interested in analyzing EEG/MEG recordings using Brainstorm. Teaching in English. |
| Documents | TBD Introduction slides | TBD Tutorial walkthrough |
Program (TBD)
This session is based on a simplified version of the xxxx
| 13:00-13:45 | Onsite assistance in installing the material for the training session |
| 13:45-14:15 | Lecture: Brainstorm overview Software structure, typical data workflow |
| 14:45-15:45 | Anatomy Database explorer MRI volumes, surfaces Anatomical parcellations Coregistration of pre- and post-implantation images |
| 15:45-16:45 | EEG recordings Reviewing continuous EEG recordings Montages and management of event markers |
| 16:45-17:45 | Advanced topics - Based on participants' requests Time-frequency analysis: Identification of ictal HFO frequency bands Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling Open discussion with Bainstorm users |
Requirements
In order to make the workshop as efficient as possible, we ask all the attendees to prepare their laptops by:
Installing and testing Brainstorm in your laptop, and
Downloading the workshop dataset prior to the workshop.
1. Install Brainstorm
Please read carefully the following instructions to download, install and test Brainstorm:
Preparing your laptop for the training
2. Workshop dataset
TBD.
Troubleshooting
For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )