= Breckenridge, Colorado, USA: March 3rd, 2025 =
<<HTML(<img align="right" alt="BreckenridgeConference" class="attachment" src="/brainstorm/WorkshopBreckenridge2025?action=AttachFile&do=get&target=Breckenridge_logo.png" title="Breckenridge_logo.png" style="width: 50%;">)>>

Full-day of lectures and a workshop on Brainstorm as part of the International Conference on [[https://www.aiepilepsy-neuro.com/|Artificial Intelligence in Epilepsy and Neurological Disorders in Breckenridge]]. 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>)>> Breckenridge<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>March 3rd, 2025, 8:30-17:45<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://www.aiepilepsy-neuro.com/register.aspx?e=1658&culture=en-US|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/JohnMosher|John Mosher]], [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani|Takfarinas Medani]], [[https://www.linkedin.com/in/yash-vakilna/|Yash Vakilna]], [[https://www.linkedin.com/in/johnson-hampson/|Johnson Hampson]] and [[https://neuroimage.usc.edu/brainstorm/AboutUs/RaymundoCassani|Raymundo Cassani]] <<BR>> (UTH/USC USA, McGill Canada )<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing sEEG/ECOG 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 | Walkthrough | 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.

== Installing Brainstorm ==
Please read carefully the following instructions on: <<BR>>[[WorkshopGeneralInstall|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.


== Program ==
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<<HTML(<TR><TD>)>> 08:30-08:55<<HTML(</TD><TD>)>>

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

<<HTML(<TR><TD>)>>08:55-09:00<<HTML(</TD><TD>)>>

'''Introduction to the Workshop - '''Richard Leahy, USC, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:00-09:20<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]] - '''John Mosher, UTH, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:20-09:40<<HTML(</TD><TD>)>>

'''Presentation - ''' Speaker, institute, Country<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:40-10:00<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]] '''- Takfarinas Medani, USC, USA<<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>)>>10:15-11:00<<HTML(</TD><TD>)>>

'''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani (Add Johnson)

''' 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>)>>11:00-12:15<<HTML(</TD><TD>)>>

'''Tutorial – Hands-On Brainstorm 2/3 - '''Y.Vakilna, C.Chinara, & T.Medani

''' Introduction to Brainstorm Interface: Functional Data: sEEG '''
===> We Recommend you bring a mouse for this section <===

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>)>>12:15-13:00<<HTML(</TD><TD>)>>

'''Lunch Break (Provided? to confirm/ ask one of the sponsor sEEG??)'''<<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''' 
==>Import precomputed Brainstorm protocol<==  
sEEG Montage Configuration
sEEG Frequency Analysis and Filtering 
Compute Forward Model (aka Head Model) 
Compute Noise Covariance Matrix  
Compute Inverse Model  
View Source Results  
Atlases and Scouts

<<HTML(<TR><TD>)>>15:00-15:15<<HTML(</TD><TD>)>>

'''Coffee Break (provided)'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:15-17:30<<HTML(</TD><TD>)>> 
'''SEEG Advanced Analysis''' 
Modeling interictal spikes  
Modeling ictal wave within the seizure window 
Modeling ictal onset with LVFA at Sensor Space 
Modeling ictal onset with LVFA at Source Space 
Modeling ictal onset with repetitive spiking at Sensor and Source spaces

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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)'''.

End of the workshop, the main conference begins at 6 pm

== Bring your own data ==
The last session will be mostly dedicated to addressing participants' requests. We encourage you to bring in your own sample of data that you would be interested in processing with Brainstorm. We may ask that you pair with other attendees, for logistics purposes.

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 ) & Chinmay ... Todo