|
Size: 6442
Comment:
|
Size: 4365
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Aix-en-Provence, France: October 4, 2021 = Half-day workshop, as part of the [[https://cuttingeeg2021.org/|CuttingEEG conference]]. This session will introduce new features for SEEG analysis. Participants will learn how to access these new tools from the Brainstorm environment on their personal laptops. |
= Los Angeles, CA, USA: October 18th, 2023 = Half-day workshop, as part of the [[https://cuttinggardens2023.org/|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. |
| Line 7: | Line 7: |
| <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>>[[https://cuttingeeg2021.org/venue/|Cube classrooms]]<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|Univerisyt of Southern California]]<<HTML(</TD></TR>)>> |
| Line 9: | Line 9: |
| <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Monday October 4th, 2021: 8:30-12:15<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Wednesday October 18th, 2023: 13:00-17:30<<HTML(</TD></TR>)>> |
| Line 11: | Line 11: |
| <<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>[[AboutUs/FrancoisTadel|Francois Tadel]]<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>[[https://neuroimage.usc.edu/brainstorm/AboutUs/RaymundoCassani|Raymundo Cassani]] & [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani#preview|Takfarinas Medani]]<<HTML(</TD></TR>)>> |
| Line 13: | Line 13: |
| <<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>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#registration|Please visit this page]]. <<HTML(</TD></TR>)>> |
| Line 15: | Line 15: |
| <<HTML(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>>[[https://neuroimage.usc.edu/resources/cuttingeeg2021_brainstorm_slides.pdf|Introduction slides]] | [[https://neuroimage.usc.edu/resources/cuttingeeg2021_brainstorm_walkthrough.pdf|Tutorial walkthrough]] <<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Audience'''''' '''<<HTML(</TD><TD>)>>Users interested in analyzing EEG/MEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>> TBD [[https://neuroimage.usc.edu/resources/cuttingeeg2021_brainstorm_slides.pdf|Introduction slides]] | TBD [[https://neuroimage.usc.edu/resources/cuttingeeg2021_brainstorm_walkthrough.pdf|Tutorial walkthrough]] <<HTML(</TD></TR>)>> |
| Line 19: | Line 21: |
| == Requirements == 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. == Installing Brainstorm == Please read carefully the following instructions on: <<BR>>[[WorkshopGeneralInstall|preparing your laptop for the training]] == Workshop dataset == The workshop dataset is a pre-processed version of the dataset in used in the [[Tutorials/Yokogawa|Brainstorm tutorial on median nerve stimulation]]. It consists of simultaneous EEG and MEG recordings during a median nerve stimulation experiment (right arm). A full description of the dataset can be found [[Tutorials/Yokogawa#Description_of_the_experiment|here]]. Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop. 1. Download the tutorial dataset (360 MB): https://box.bic.mni.mcgill.ca/s/iNxszVo7q8rSXwB 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshop_lax`'''. 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) * '''`workshop_lax`''': Dataset used during the workshop session |
|
| Line 20: | Line 42: |
| This session is based on a simplified version of the [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity|SEEG/Epileptogenicity tutorial]]. |
|
| Line 24: | Line 44: |
| <<HTML(<TR><TD>)>>8:30-9:15<<HTML(</TD><TD>)>>Onsite assistance in installing the material for the training session <<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>13:00-13:45<<HTML(</TD><TD>)>>Onsite assistance in installing the material for the training session <<HTML(</TD></TR>)>> |
| Line 26: | Line 46: |
| <<HTML(<TR><TD>)>>9:15-9:45<<HTML(</TD><TD>)>>'''Lecture: Brainstorm overview''' | <<HTML(<TR><TD>)>>13:45-14:15<<HTML(</TD><TD>)>>'''Lecture: Brainstorm overview''' |
| Line 30: | Line 50: |
| Presentation of the example dataset (BIDS-iEEG) |
|
| Line 34: | Line 52: |
| <<HTML(<TR><TD>)>>9:45-10:45<<HTML(</TD><TD>)>>'''Anatomy''' | <<HTML(<TR><TD>)>>14:45-15:45<<HTML(</TD><TD>)>>'''Anatomy''' |
| Line 44: | Line 62: |
| <<HTML(<TR><TD>)>>10:45-11:45<<HTML(</TD><TD>)>>'''SEEG recordings''' | <<HTML(<TR><TD>)>>15:45-16:45<<HTML(</TD><TD>)>>'''EEG recordings''' |
| Line 46: | Line 64: |
| Reviewing continuous SEEG recordings | Reviewing continuous EEG recordings |
| Line 50: | Line 68: |
| Marking SEEG contacts on post-implantation image Anatomical labelling of SEEG contacts <<HTML(<TR><TD>)>>11:45-12:15<<HTML(</TD><TD>)>>'''Advanced topics - Based on participants' requests''' |
<<HTML(<TR><TD>)>>16:45-17:45<<HTML(</TD><TD>)>>'''Advanced topics - Based on participants' requests''' |
| Line 70: | Line 84: |
| ---- = 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"'''. * 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. * Don't forget your '''power adapter'''! == 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. 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}} |
|
| Line 167: | Line 86: |
| 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 |
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.
Installing Brainstorm
Please read carefully the following instructions on:
preparing your laptop for the training
Workshop dataset
The workshop dataset is a pre-processed version of the dataset in used in the Brainstorm tutorial on median nerve stimulation. It consists of simultaneous EEG and MEG recordings during a median nerve stimulation experiment (right arm). A full description of the dataset can be found here.
Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop.
- Download the tutorial dataset (360 MB):
Unzip the downloaded file on your desktop: it will create a new folder named workshop_lax.
- 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)
workshop_lax: Dataset used during the workshop session
Program
| 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 |
Troubleshooting
For any technical problem, please contact Raymundo Cassani (raymundo.cassani@mcgill.ca)