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= Park City, Utah, USA: April 1st, 2024 =
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Half-day workshop as part of the International Conference on Artificial Intelligence in Epilepsy and Neurological Disorders in Park City  https://www.aiepilepsy-neuro.com/. This session will be an introduction to 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>)>> [[https://www.aiepilepsy-neuro.com/content.aspx?e=1658&c=17242&culture=en-US|Park City]]<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>April 1st, 2024, 9:00-17:00<<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/|IA EPILEPSY 2024]] <<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]] and TBA <<BR>> (UTH/USC, USA)<<HTML(</TD></TR>)>>

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

<<HTML(<!--<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> TBD [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Lectures slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Walkthrough]] | [[https://forms.gle/XXXXXXXX|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]]

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== Workshop dataset ==
TBD

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://box.bic.mni.mcgill.ca/s/XXXXX
 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshop_XXXX`'''
 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)
  * '''`workshop_XXXX`''': Dataset used during the workshop session
}}}
== Program ==
=== April 1st ===
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<<HTML(<TR><TD>)>>08:30-09:00<<HTML(</TD><TD>)>> Registration <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:00-12:00<<HTML(</TD><TD>)>> Lectures <<HTML(</TD></TR>)>>

<<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>)>>13:00-13:30<<HTML(</TD><TD>)>>

Lecture: Brainstorm overview

Software structure, typical data workflow

Presentation of the example dataset (BIDS-iEEG)

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

Anatomy

Database explorer

MRI volumes, surfaces

Anatomical parcellations

Coregistration of pre- and post-implantation images

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<<HTML(<TR><TD>)>>14:30-15:30<<HTML(</TD><TD>)>>

SEEG recordings

Reviewing continuous SEEG recordings

Montages and management of event markers

Marking SEEG contacts on post-implantation image

Anatomical labelling of SEEG contacts

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<<HTML(<TR><TD>)>>15:30-16:30<<HTML(</TD><TD>)>>

Advanced topics - Based 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 Bainstorm users

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=== Day 2 ===
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<<HTML(<TR><TD>)>>08:30-09:00<<HTML(</TD><TD>)>>'''Source modelling''' ''(Lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:00-10:45<<HTML(</TD><TD>)>>'''Sources estimation'''

Forward model (aka Head model)

Noise covariance matrix

Source estimation (surfaces and volume source spaces)

Cortex parcellations: Atlases and Scouts

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<<HTML(<TR><TD>)>>10:45-12:00<<HTML(</TD><TD>)>>'''Subject level statistics'''

Statistics, sensor space

Statistics, source space

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<<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>'''ACRI Visiting Scholars Research Seminar''' ''(Lecture S. Baillet)'' <<BR>> Lunch will be provided <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:00-14:30<<HTML(</TD><TD>)>>'''Subject level analysis'''

Subject averages (sensors, time-frequency and sources)

Within subject differences

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<<HTML(<TR><TD>)>>14:30-16:00<<HTML(</TD><TD>)>>'''Group level analysis'''

Preparing sensor, time-frequency and sources data

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=== Day 3 ===
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<<HTML(<TR><TD>)>>09:00-09:30<<HTML(</TD><TD>)>>'''Connectivity & resting-state & evoked response''' ''(Lecture S. Baillet)''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:30-10:00<<HTML(</TD><TD>)>>'''Connectivity'''

Functional connectivity

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<<HTML(<TR><TD>)>>10:00-11:00<<HTML(</TD><TD>)>>'''Beyond the GUI'''

Scripting

GitHub

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<<HTML(<TR><TD>)>>11:00-12:00<<HTML(</TD><TD>)>>'''Participants working with their own data'''<<HTML(</TD></TR>)>>

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

<<HTML(<TR><TD>)>>12:00-15:30<<HTML(</TD><TD>)>>'''Participants working with their own data'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:30-16:00<<HTML(</TD><TD>)>>'''Wrap-up'''

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== 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 MEG/EEG 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 ==