= Toulouse, France: Monday, March 19th, 2025 =
<<HTML(<img align="right" alt="ToulouseConference" class="attachment" src="/brainstorm/WorkshopToulouse2025?action=AttachFile&do=get&target=micmiac2025.png" title="Toulouse_logo.png" style="width: 50%;">)>>

4 hours of lectures and a workshop on Brainstorm as part of the [[https://micmac-workshop.org/ | MicMac Conference in Toulouse, France]], a scientific event focused on intracranial electrophysiological recordings using micro- and macro-electrodes.
This session will be hands-on Brainstorm features for sEEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops.

== General information ==
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<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> Toulouse<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>March 19th, 2025, 10:30-16:00<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://micmac-workshop.org/register/|Please visit this page]]. <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>''' '''[[https://www.aiepilepsy-neuro.com/|AI EPILEPSY 2025]] <<BR>> <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Instructors'''<<HTML(</TD><TD>)>>  [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani|Takfarinas Medani]], and [[https://www.neurotrack.fr/|Anne Sophie Dubarry]] <<BR>> (UTH/USC USA)<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing sEEG recordings using Brainstorm.<<BR>>Some experience with iEEG and signal processing is recommended. Teaching in English.<<BR>>Number of participants: XX <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> Intro slides | [[toDo|Walkthrough]] | [[TBDA: https://docs.google.com/forms/d/e/1FAIpQLSfLM_V2LISKa-ZPKUqrh6s4ezWFbpnUIBuLyIC1Tehw7GjZdw/viewform?usp=sf_link|Survey]]<<HTML(</TD></TR>)>>

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== 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.

{{{#!wiki tip

We highly recommend bringing an '''external mouse''' on the workshop day. Most of the manipulations are done with the mouse, and some involve an intense use of the scrolling operation.
}}}
== Installing Brainstorm ==
Please read carefully the following instructions on: <<BR>>[[WorkshopGeneralInstall|preparing your laptop for the training]]

== Workshop dataset ==
In this workshop, we will work on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston. The link to download the data and protocol will be provided soon.

== Program ==
=== Wednesday, March 19th, 2025 ===
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<<HTML(<TR><TD>)>> 10:00-10:30 <<HTML(</TD><TD>)>>

'''Registration & Check in'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:30-11:15<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview & BioPhysics of SEEG]] '''- Takfarinas Medani, USC, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>11:15-11:30<<HTML(</TD><TD>)>>

'''Coffee Break<<BR>>'''Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>11:30-12:00<<HTML(</TD><TD>)>>

'''Tutorial – Hands-On Brainstorm - ''' 

''' Introduction to Brainstorm Interface: Anatomy Data '''

Database explorer

MRI volumes, surfaces

Anatomical parcellations

CT volumes Coregistration: pre- / post-implantation images <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>12:00-12:30<<HTML(</TD><TD>)>>

'''Tutorial – Hands-On Brainstorm - '''

''' Introduction to Brainstorm Interface: sEEG Functional Data. '''

Manual marking of SEEG contacts on post-implantation image

Automatic marking of SEEG contacts on post-implantation image

Automatic anatomical labeling of SEEG contacts

Reviewing continuous SEEG recordings

Montages and management of event markers

<<HTML(<TR><TD>)>>12:30-13:30<<HTML(</TD><TD>)>>

'''Lunch Break'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:30-14:30<<HTML(</TD><TD>)>> '''SEEG: Analysis'''

==>Import precomputed Brainstorm protocol<==

sEEG Montage Configuration

sEEG Frequency Analysis and Filtering

Compute Forward Model (aka the Head or Lead Field Model)

Compute Noise Covariance Matrix

Compute Inverse Model

View Source Results

Atlases and Scouts

<<HTML(<TR><TD>)>>14:30-16:00<<HTML(</TD><TD>)>>
'''SEEG: Advanced Analysis'''

Modeling interictal spikes

Modeling ictal wave within the seizure window

Modeling ictal onset with LVFA in the Sensor Space

Modeling ictal onset with LVFA in the Source Space

Modeling ictal onset with repetitive spiking at Sensor and Source spaces

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<<HTML(<TR><TD>)>>16:00<<HTML(</TD><TD>)>>

End of the workshop

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We will provide a [[XXXX|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)'''.

== Bring your own data ==
At the end of the session, the Brainstorm team will dedicate their time to address participants' requests. We encourage you to bring in your own sample of data that you would be interested in processing with Brainstorm.

The file formats that can be read by Brainstorm are listed on the [[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|Introduction page]]. Please contact us in advance if you are not sure your dataset can be imported in Brainstorm. If you do not have data available, you may continue to use the tutorial dataset used in the present workshop.

{{{#!wiki comment



We provide [[https://box.bic.mni.mcgill.ca/s/XXXX|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]].
}}}
== Troubleshooting ==
For any technical problem, please contact Takfarinas Medani ( medani@usc.edu )