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| = Los Angeles, CA, USA: October 18th, 2023 = <<HTML(<img align="right" alt="cutting_lax_logo.png" class="attachment" src="/brainstorm/WorkshopLA2023?action=AttachFile&do=get&target=cutting_lax_logo.png" title="cutting_lax_logo.png" style="width: 35%;">)>> |
= Los Angeles, CA, USA: December 5th, 2024, === REGISTRATION IS NOW OPEN - Limited Places === = The full-day workshop will take place at [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]], on Dec 5th, a day prior to the [[https://aesnet.org/AES-annual-meeting|AES2024 Meeting]]. <<BR>> This session will introduce Brainstorm for multimodal data analysis (EEG/MEG) in the morning, and a focus on the iEEG analysis in the afternoon. |
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| Half-day workshop, as part of the [[https://cuttinggardens2023.org/|CuttingGardens2023 conference]]. <<BR>> This session will be an introduction to Brainstorm for EEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops. The link to the video will be uploaded soon. | Participants will learn how to use Brainstorm and access its new tools on their personal laptops. Registration is now open, please visit this [[https://my.cheddarup.com/c/brainstormworkshopla2024/items?cart|page]] to register, there is a limited number of places. |
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| <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Wednesday October 18th, 2023: 13:00-17:30<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Thursday December 5th, 2024, 8:30-17:30<<HTML(</TD></TR>)>> |
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| <<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>)>> | <<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>Brainstorm team<<HTML(</TD></TR>)>> |
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| <<HTML(<!--<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#registration|Please visit this page]]. <<HTML(</TD></TR>-->)>> | <<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://my.cheddarup.com/c/brainstormworkshopla2024/items?cart|Registration is now open]]. <<HTML(</TD></TR>)>> |
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| <<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>)>>'''Audience'''''' '''<<HTML(</TD><TD>)>>Users interested in analyzing iEEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>> |
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| 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]]. | In this workshop, we will be working on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston. |
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| Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop. | The data is distributed as '''raw''' and '''pre-processed''' data. |
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| 1. Download the tutorial dataset (360 MB): . https://box.bic.mni.mcgill.ca/s/hKO5zc2W4uDE3Zk 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshop_lax`''' |
1. '''raw data''' is located in the file '''`WorkshopXXX_raw.zip`''' which contains raw SEEG recordings (in EDF format), T1 MRI and CT scan (both in NIfTI format). The raw SEEG recordings correspond to: a. Two files containing seizure onset: i. Seizure onset with Low-voltage-fast-activity i. Seizure with Ictal repetitive spiking a. One file with interictal spike, and a. One file containing baseline recordings 1. '''pre-processed data''' is located in the file '''`WorkshopXXX_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed. Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the data to be used in the workshop. 1. Download the '''raw data''': . TBD 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopUTAH_raw`''' 1. Download the '''pre-processed data'''. Do not unzip this file: . TBD |
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| * '''`workshop_lax`''': Dataset used during the workshop session | * '''`workshopXXX_raw`''': Raw data, for SEEG localization demonstration * '''`WorkshopXXX_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session |
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| == Program == | == Program (TBD) == |
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| <<HTML(<TR><TD>)>>12:30-13:00<<HTML(</TD><TD>)>>Onsite assistance in installing the material for the training session <<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>> 08:30-09:00<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>13:00-13:30<<HTML(</TD><TD>)>>Introduction to Brainstorm (lecture)<<HTML(</TD></TR>)>> | '''Registration & Check in'''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>13:30-14:35<<HTML(</TD><TD>)>>'''Loading anatomy and recordings''' | <<HTML(<TR><TD>)>>09:00-09:05<<HTML(</TD><TD>)>> '''Introduction to the Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:05-09:35<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of MEG/EEG/SEEG]] -'''John Mosher, UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:35-10:00<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]]'''-Sylvain Baillet, McGill, Canada<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>10:00-10:15<<HTML(</TD><TD>)>> '''Coffee Break<<BR>>'''Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>10:15-10:45<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani '''Anatomy &''' '''Functional data''' Database explorer MRI volumes, surfaces, Anatomical parcellations . Review raw data, event markers, EEG/MEG sensors <<HTML(<TR><TD>)>>10:45-12:15<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 2/3 - '''Y.Vakilna, C.Chinara, & T.Medani '''Loading anatomy and recordings''' |
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| <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>14:35-15:35<<HTML(</TD><TD>)>>'''Pre-processing''' |
'''Pre-processing''' |
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| Artifact correction with SSP <<HTML(</TD></TR>)>> | Artifact correction with SSP |
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| <<HTML(<TR><TD>)>>15:35-15:50<<HTML(</TD><TD>)>>''Coffee break''<<HTML(</TD></TR>)>> <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>15:50-16:20<<HTML(</TD><TD>)>>'''Analysis sensor level''' |
'''Analysis sensor level''' |
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| <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>16:20-16:55<<HTML(</TD><TD>)>>'''Source estimation''' |
'''Source estimation''' |
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| Source estimation (from EEG and MEG recordings) | Source estimation '''Analysis source level''' Cortex parcellation: Atlas and Scouts <<HTML(<TR><TD>)>>12:15-13:00<<HTML(</TD><TD>)>> '''Lunch Break (Provided)'''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>13:00-15:00<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 3/3 - '''Y.Vakilna, C.Chinara, & T.Medani '''SEEG recordings''' Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image |
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| <<HTML(<TR><TD>)>>16:55-17:15<<HTML(</TD><TD>)>>'''Analysis source level''' | <<HTML(<TR><TD>)>>15:00-15:15<<HTML(</TD><TD>)>> |
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| Cortex parcellations: Atlases and Scouts | '''Coffee Break'''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>15:15-17:00<<HTML(</TD><TD>)>> '''Advanced topics - SEEG AnalsysisBased 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 Brainstorm team/users |
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| We provide [[https://box.bic.mni.mcgill.ca/s/rpkrUdfXUSxjArh|a detailed step-by-step walkthrough]] of the data analyses performed at the training. In addition, results obtained in this workshop can be replicated with [[https://box.bic.mni.mcgill.ca/s/kYKqad5wzYabzq1|this script]]. | We will provide [[https://box.bic.mni.mcgill.ca/s/rpkrUdfXUSxjArh|a detailed step-by-step walkthrough]] of the data analyses performed at the training. In addition, results obtained in this workshop can be replicated with [[https://box.bic.mni.mcgill.ca/s/kYKqad5wzYabzq1|this script]]. |
Los Angeles, CA, USA: December 5th, 2024, === REGISTRATION IS NOW OPEN - Limited Places ===
The full-day workshop will take place at University of Southern California, on Dec 5th, a day prior to the AES2024 Meeting.
This session will introduce Brainstorm for multimodal data analysis (EEG/MEG) in the morning, and a focus on the iEEG analysis in the afternoon.
Participants will learn how to use Brainstorm and access its new tools on their personal laptops.
Registration is now open, please visit this page to register, there is a limited number of places.
General information
| Where | University of Southern California |
| When | Thursday December 5th, 2024, 8:30-17:30 |
| Instructor | Brainstorm team |
| Registration | Registration is now open. |
| Audience | Users interested in analyzing iEEG recordings using Brainstorm. Teaching in English. |
| Documents | Introduction 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.
Installing Brainstorm
Please read carefully the following instructions on:
preparing your laptop for the training
Workshop dataset
In this workshop, we will be working on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston.
The data is distributed as raw and pre-processed data.
raw data is located in the file WorkshopXXX_raw.zip which contains raw SEEG recordings (in EDF format), T1 MRI and CT scan (both in NIfTI format). The raw SEEG recordings correspond to:
- Two files containing seizure onset:
- Seizure onset with Low-voltage-fast-activity
- Seizure with Ictal repetitive spiking
- One file with interictal spike, and
- One file containing baseline recordings
- Two files containing seizure onset:
pre-processed data is located in the file WorkshopXXX_precomputed.zip, which contains a Brainstorm protocol with the raw data already pre-processed.
Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the data to be used in the workshop.
Download the raw data:
- TBD
Unzip the downloaded raw data on your desktop: it will create a new folder named workshopUTAH_raw
Download the pre-processed data. Do not unzip this file:
- TBD
- 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)
workshopXXX_raw: Raw data, for SEEG localization demonstration
WorkshopXXX_precomputed.zip: Pre-processed Brainstorm protocol for workshop session
Program (TBD)
| 08:30-09:00 | Registration & Check in |
| 09:00-09:05 | Introduction to the Workshop–Richard Leahy, USC, USA |
| 09:05-09:35 | BioPhysics of MEG/EEG/SEEG -John Mosher, UTH, USA |
| 09:35-10:00 | Brainstorm Overview-Sylvain Baillet, McGill, Canada |
| 10:00-10:15 | Coffee Break |
| 10:15-10:45 | Tutorial – Hands-On Brainstorm 1/3 - Y.Vakilna, C.Chinara, & T.Medani Anatomy & Functional data Database explorer MRI volumes, surfaces, Anatomical parcellations
|
| 10:45-12:15 | Tutorial – Hands-On Brainstorm 2/3 - Y.Vakilna, C.Chinara, & T.Medani Loading anatomy and recordings Set anatomy Review RAW recordings Import events Pre-processing Frequency filters Artifact detection Artifact correction with SSP Analysis sensor level Import recordings Review trials Trial averages Source estimation Forward model (aka Head model) Noise covariance matrix Source estimation Analysis source level Cortex parcellation: Atlas and Scouts |
| 12:15-13:00 | Lunch Break (Provided) |
| 13:00-15:00 | Tutorial – Hands-On Brainstorm 3/3 - Y.Vakilna, C.Chinara, & T.Medani SEEG recordings Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image |
| 15:00-15:15 | Coffee Break |
| 15:15-17:00 | Advanced topics - SEEG AnalsysisBased 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 Brainstorm team/users |
We will provide a detailed step-by-step walkthrough of the data analyses performed at the training. In addition, results obtained in this workshop can be replicated with this script.
Troubleshooting
For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )