= Los Angeles, CA, USA: December 5th, 2024 =
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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.

== General information ==
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<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]]<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Thursdya December 5th, 2024: 8:30-17:30<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>Brainstrom team<<HTML(</TD></TR>)>>

<<HTML(<!--<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#registration|T]]BD. <<HTML(</TD></TR>-->)>>

<<HTML(<TR><TD>)>>'''Audience'''''' '''<<HTML(</TD><TD>)>>Users interested in analyzing iEEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>>

<<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>)>>

== 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.

 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:
  a. Two files containing seizure onset:
   i. Seizure onset with Low-voltage-fast-activity
   i. Seizure with Ictal repetitive spiking
  a. One file with interictal spike, and
  a. One file containing baseline recordings

 1. '''pre-processed data''' is located in the file '''`WorkshopXXX_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.

 1. Download the '''raw data''':
  . TBD
 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopUTAH_raw`'''

 1. Download the '''pre-processed data'''. Do not unzip this file:
  . TBD

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

== Program ==
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<<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>)>>Introduction to Brainstorm (lecture)<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:30-14:35<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''

Set anatomy

Review RAW recordings

Import events

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<<HTML(<TR><TD>)>>14:35-15:35<<HTML(</TD><TD>)>>'''Pre-processing'''

Frequency filters

Artifact detection

Artifact correction with SSP <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:35-15:50<<HTML(</TD><TD>)>>''Coffee break''<<HTML(</TD></TR>)>>

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<<HTML(<TR><TD>)>>15:50-16:20<<HTML(</TD><TD>)>>'''Analysis sensor level'''

Import recordings

Review trials

Trial averages

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<<HTML(<TR><TD>)>>16:20-16:55<<HTML(</TD><TD>)>>'''Source estimation'''

Forward model (aka Head model)

Noise covariance matrix

Source estimation (from EEG and MEG recordings)

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<<HTML(<TR><TD>)>>16:55-17:15<<HTML(</TD><TD>)>>'''Analysis source level'''

Cortex parcellations: Atlases and Scouts

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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]].

== Troubleshooting ==
For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )