= Breckenridge, Colorado, USA: Monday, 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/ChinmayChinara|Chinmay Chinara]] <<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: 30 <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Slides/TakfarinasMedani_IntroSlides.pdf|Intro slides]] | [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Walkthrough-Workshop-Colorado-2025.pdf|Walkthrough]] | [[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 day of the workshop. 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 be working on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston.

 1. The data is distributed as '''raw''' and '''pre-processed''' data.
  a. '''raw data''' is located in the file '''`WorkshopBreckenridge_raw.zip`''' which  contains raw SEEG recordings (in EDF format), T1 MRI, T2 FLAIR MRI, Diffusion Weighted MRI and CT scan (all in NIfTI-1 format). The raw SEEG recordings correspond to:
   i. Two files containing seizure onset:
    * Seizure onset with Low-voltage-fast-activity
    * Seizure with Ictal repetitive spiking
   i. One file with interictal spike, and
   i. One file containing baseline recordings

  a. '''pre-processed data''' is located in the file '''`WorkshopBreckenridge_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed.

 1. Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the data to be used in the workshop.
  a. Download the '''raw data (512 MB)''':
   * [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Data/WorkshopBreckenridge_raw.zip|WorkshopBreckenridge_raw.zip]].<<BR>>Unzip the downloaded raw data on your desktop: it will create a new folder named '''`WorkshopBreckenridge_raw`'''

  a. Download the '''pre-processed data (3.5 GB)'''. Do not unzip this file:
   * [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Data/WorkshopBreckenridge_precomputed.zip|WorkshopBreckenridge_precomputed.zip]]

 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)
  * '''`WorkshopBreckenridge_raw.zip`''': Raw data, for SEEG localization demonstration
  * '''`WorkshopBreckenridge_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session

== Brainstorm prerelease ==
We are also excited to offer early access to a version that's still in development, designed specifically for gathering your invaluable feedback on features and usability featuring Automatic SEEG contact localization and labeling.

{{{#!wiki important
This is a prerelease version, and while we’ve built it with care, it may not be completely stable. We're offering it solely to gain insights from real user experiences. Your participation will directly impact improvements and feature enhancements in the final release.
}}}
 1. The prerelease compiled executable with the associated data:<<BR>>  [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Software/brainstorm_250301_prerelease_bin.zip|brainstorm_250301_prerelease_bin.zip]] <<BR>>Unzip on your desktop: it will create a new folder named '''`brainstorm_250301_prerelease_bin`''' with contents as under:
  * '''`brainstorm3`''': the software folder, containing the '''prerelease''' compiled executable
  * '''`data`''': pre-implantation T1 MRI and post-implantation CT scans (both in NIfTI-1 format)
  * Follow the same installation instructions as mentioned in the top of this page.

 1. Walkthrough video showing features to explore in this prerelease:<<BR>>'''[[https://www.youtube.com/watch?v=ixyH4DqNU6E|Automatic SEEG contact localization and labeling (Brainstorm+GARDEL)]]'''

== Program ==
=== Monday, March 3, 2025 ===
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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 - '''John Mosher, USC, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:00-09:30<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Slides/JohnMosher_Slides.pdf|BioPhysics of SEEG]] - '''John Mosher, UTH, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:30-09:45<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Slides/YashVakilna_Slides.pdf|Sensor & source space modeling of epileptiform activity]] - '''Yash Vakilna, UTH, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:45-09:55<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Slides/AnandJoshi_Slides.pdf|Automatic Delineation of Surgical Resection]] - '''Anand Joshi , USC, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:55-10:25<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Slides/TakfarinasMedani_IntroSlides.pdf|Brainstorm Overview]] '''- Takfarinas Medani, USC, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:25-10:30<<HTML(</TD><TD>)>>

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

<<HTML(<TR><TD>)>>10:30-11:00<<HTML(</TD><TD>)>>

'''Tutorial – Hands-On Brainstorm 1/4 - ''' Y.Vakilna, C.Chinara, J.Hampson & T.Medani

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

Database explorer

MRI volumes, surfaces

Anatomical parcellations

CT volumes Coregistration: pre- / post-implantation images

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

'''Tutorial – Hands-On Brainstorm 2/4 - ''' Y.Vakilna, C.Chinara, J.Hampson & T.Medani

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

'''Lunch Break (Not Provided - Please check options [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/breckenridge_conf_map.pdf|here]])'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:00-15:00<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 3/4 - ''' Y.Vakilna, C.Chinara, J.Hampson & T.Medani

'''SEEG: Analysis'''

==>Import precomputed Brainstorm protocol<==

Preprocessing & Exporting

 * Remove Power Line Noise
 * Import Recordings
 * sEEG Montage Configuration

Modeling Interictal Spikes Modeling ictal wave within the seizure window

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

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

<<HTML(<TR><TD>)>>15:15-17:30<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 4/4 - '''Y.Vakilna, C.Chinara, J.Hampson & T.Medani

'''SEEG: Advanced Analysis'''

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

 * Compute Source Model
 * Extract Scout Time Series
 * Compute Time-Frequency Decomposition

Pre- / post-MRI volume resection delineation

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<<HTML(<TR><TD>)>>17:30<<HTML(</TD><TD>)>>

End of the workshop, main conference begins at 6pm

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We will provide a [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Walkthrough-Workshop-Colorado-2025.pdf|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 )