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| = Register Now: seats are very limited! = <<HTML(<img align="right" alt="LA2024_logo" class="attachment" src="/brainstorm/WorkshopLA2024?action=AttachFile&do=get&target=LA2024_logo.png" title="LA2024_logo.png" style="width: 45%;">)>> |
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| <<HTML(<img align="right" alt="USC.jpg" class="attachment" src="/brainstorm/WorkshopLA2024?action=AttachFile&do=get&target=cutting_lax_logo.png" title="USC.jpg" style="width: 35%;">)>> | This full-day workshop will take place at the [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]] on Dec 5th, immediately prior to the American Epilepsy Society Meeting ([[https://aesnet.org/AES-annual-meeting|AES 2024)]]. This session will highlight Brainstorm's unique features for multimodal scalp electrophysiology data analysis (EEG/MEG), with a second focus on intracranial recordings (iEEG). |
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| Full-day workshop, prior of the [[https://aesnet.org/AES-annual-meeting|AES2023 Meeting]]. <<BR>> This session will be an introduction to Brainstorm for iEEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops. | Participants are invited to their personal laptops for a unique hands-on experience (data will be provided). Registration is now open via this [[https://my.cheddarup.com/c/brainstormworkshopla2024/items?cart|page]]. |
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| <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Thursdya December 5th, 2024, 8:30-17:30<<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>)>>Brainstrom team<<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|T]]BD. <<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>)>>'''Documents'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/XRahw8lOSpgFetj|Introduction slides]] | [[https://box.bic.mni.mcgill.ca/s/rpkrUdfXUSxjArh|Walkthrough]] | [[https://forms.gle/R4g5w1A3aUNz8jMB9|Survey]] <<HTML(</TD></TR>)>> <<HTML(</TABLE>)>> | <<HTML(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/XRahw8lOSpgFetj|Introduction slides]] | [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Walkthrough_lax_workshop_2024_v0.pdf|Walkthrough]] |[[https://forms.gle/JfafQxq4NPnDKdGaA|Survey]]<<HTML(</TD></TR>)>> <<HTML(</TABLE>)>> |
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| {{{#!wiki tip '''We highly recommend bringing an external mouse on the day of the workshop. Most of the manipulations are done with the mouse, and some involve an intense use of the scrolling operation.''' }}} |
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| In this workshop, we will be working on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston. | In this workshop, we will be working on a multimodal data. In the morning session we will work on combined EEG/MEG data sets. In the afternoon we will use SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston. === Morning Session (EEG and MEG Analysis) === The workshop dataset for this session is a pre-processed version of the dataset 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://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Data/workshopLaxMorning.zip|workshopLaxMorning.zip]] 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshopLaxMorning`''' 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) * '''`workshopLaxMorning.zip`''': Dataset used during the workshop session === Afternoon Session (SEEG Analysis) === In this session of the workshop, we will be working on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston. |
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| 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: | 1. '''raw data''' is located in the file '''`WorkshopLaxAfternoon_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: |
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| 1. '''pre-processed data''' is located in the file '''`WorkshopXXX_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed. | 1. '''pre-processed data''' is located in the file '''`workshopLaxAfternoon_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed. |
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| . TBD 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopUTAH_raw`''' |
. [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Data/workshopLaxAfternoon_raw.zip|workshopLaxAfternoon_raw.zip]] 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopLaxAfternoon_raw`''' |
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| . TBD | . [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Data/workshopLaxAfternoon_precomputed.zip|workshopLaxAfternoon_precomputed.zip]] |
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| * '''`workshopXXX_raw`''': Raw data, for SEEG localization demonstration * '''`WorkshopXXX_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session |
* '''`workshopLaxAfternoon_raw.zip`''': Raw data, for SEEG localization demonstration * '''`workshopLaxAfternoon_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session |
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| == Program (TBD) == | == Program == |
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| <<HTML(<TR><TD>)>> 09:30-10:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>> 08:30-09:00<<HTML(</TD><TD>)>> |
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| '''Registration, check in'''<<HTML(</TD></TR>)>> | '''Registration & Check in'''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>10:00-10:05<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:00-09:05<<HTML(</TD><TD>)>> |
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| '''Introduction to Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> | '''Introduction to the Workshop - '''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>10:05-10:35<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:05-09:35<<HTML(</TD><TD>)>> |
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| '''SEEG and the Human Brain Project-'''Philippe Ryvlin, CHUV, Switzerland<<HTML(</TD></TR>)>> | '''[[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>)>> |
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| <<HTML(<TR><TD>)>>10:35-11:05<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:35-10:00<<HTML(</TD><TD>)>> |
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| '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]]-'''John Mosher, UTH, USA<<HTML(</TD></TR>)>> | '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]] '''- Sylvain Baillet, McGill, Canada<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>11:05-11:15<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:00-10:15<<HTML(</TD><TD>)>> |
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| '''Coffee Break'''<<HTML(</TD></TR>)>> | '''Coffee Break<<BR>>'''Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>11:15-11:30<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:15-10:45<<HTML(</TD><TD>)>> |
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| '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]]'''-Sylvain Baillet, McGill, Canada | '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani |
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| <<HTML(<TR><TD>)>>11:30-12:00<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/ManishShah_slides.pdf|Source Localization on Brainstorm]]'''-Manish Shah, UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:00-12:30<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JayGavvala_slides.pdf|SEEG and Multimodality Clinical Applications in Brainstorm]]'''–Jay Gavvala, UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:30-13:15<<HTML(</TD><TD>)>> '''Lunch Break (Not Provided)'''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:45-13:15<<HTML(</TD><TD>)>> Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>> <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>13:15-16:45<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm - '''Y.Vakilna, J.Hampson, T.Medani & R.Cassani <<HTML(<TR><TD>)>>13:15-14:45<<HTML(</TD><TD>)>> '''Anatomy''' |
'''Introduction to Brainstorm Interface''' |
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| MRI volumes, surfaces | Loading anatomy and recordings |
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| Anatomical parcellations | Review MRI volumes, surfaces, Anatomical parcellations |
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| Coregistration of pre- and post-implantation images | Review raw data, event markers, EEG/MEG sensors |
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| <<HTML(<TR><TD>)>>14:45-15:30<<HTML(</TD><TD>)>> | '''Tutorial – Hands-On Brainstorm 2/3 - '''Y.Vakilna, C.Chinara, & T.Medani |
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| '''SEEG recordings''' | '''EEG and MEG Analysis''' Review RAW recordings & events Frequency filters Artifact detection & correction '''Analysis sensor level''' Import recordings Review trials Trial averages '''Source estimation''' Forward model (aka Head model) Noise covariance matrix Source estimation <<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 Analysis''' |
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| Anatomical labeling of SEEG contacts |
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| '''Advanced topics - Based on participants' requests''' | '''Advanced topics - SEEG Analsysis''' |
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| FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling Open discussion with Brainstorm 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://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Walkthrough_lax_workshop_2024_v0.pdf|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 (to be updated)'''. |
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| For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca ) | For any technical problem, please contact Takfarinas Medani ( medani@usc.edu ) |
Los Angeles, CA, USA: December 5th, 2024
Register Now: seats are very limited!
This full-day workshop will take place at the University of Southern California on Dec 5th, immediately prior to the American Epilepsy Society Meeting (AES 2024). This session will highlight Brainstorm's unique features for multimodal scalp electrophysiology data analysis (EEG/MEG), with a second focus on intracranial recordings (iEEG).
Participants are invited to their personal laptops for a unique hands-on experience (data will be provided).
Registration is now open via this page.
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
We highly recommend bringing an external mouse on the day of the workshop. Most of the manipulations are done with the mouse, and some involve an intense use of the scrolling operation.
Workshop dataset
In this workshop, we will be working on a multimodal data. In the morning session we will work on combined EEG/MEG data sets. In the afternoon we will use SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston.
Morning Session (EEG and MEG Analysis)
The workshop dataset for this session is a pre-processed version of the dataset 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 workshopLaxMorning
- 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)
workshopLaxMorning.zip: Dataset used during the workshop session
Afternoon Session (SEEG Analysis)
In this session of the 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 WorkshopLaxAfternoon_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 workshopLaxAfternoon_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:
Unzip the downloaded raw data on your desktop: it will create a new folder named workshopLaxAfternoon_raw
Download the pre-processed data. Do not unzip this file:
- 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)
workshopLaxAfternoon_raw.zip: Raw data, for SEEG localization demonstration
workshopLaxAfternoon_precomputed.zip: Pre-processed Brainstorm protocol for workshop session
Program
| 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 Introduction to Brainstorm Interface Database explorer Loading anatomy and recordings Review MRI volumes, surfaces, Anatomical parcellations Review raw data, event markers, EEG/MEG sensors |
| 10:45-12:15 | Tutorial – Hands-On Brainstorm 2/3 - Y.Vakilna, C.Chinara, & T.Medani EEG and MEG Analysis Review RAW recordings & events Frequency filters Artifact detection & correction Analysis sensor level Import recordings Review trials Trial averages Source estimation Forward model (aka Head model) Noise covariance matrix Source estimation |
| 12:15-13:00 | Lunch Break (Provided) |
| 13:00-15:00 | Tutorial – Hands-On Brainstorm 3/3 - Y.Vakilna, C.Chinara, & T.Medani SEEG Analysis 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 Analsysis Time-frequency analysis: Identification of ictal HFO frequency bands Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways |
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 (to be updated).
Troubleshooting
For any technical problem, please contact Takfarinas Medani ( medani@usc.edu )