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Park City, Utah, USA: April 1st, 2024

ParkCityConference

Full-day of lectures and a workshop on Brainstorm as part of the International Conference on Artificial Intelligence in Epilepsy and Neurological Disorders in Park City. 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

Where	Park City
When	April 1st, 2024, 8:30-17:00
Registration	Please visit this page.
Organizers	AI EPILEPSY 2024
Instructors	John Mosher, Takfarinas Medani and TBA (UTH/USC, USA)
Audience	Users interested in analyzing sEEG/ECOG recordings using Brainstorm. Some experience with iEEG and signal processing is recommended. Teaching in English. Number of participants: XX
Slides	TBD Intro slides \| Lectures slides \| Walkthrough \| Survey

Requirements

In order to make the workshop as efficient as possible, we ask all the attendees to: download, install and test the software and download the workshop dataset on their laptops prior to the workshop.

Installing Brainstorm

Please read carefully the following instructions on:
preparing your laptop for the training

Program

April 1st

09:30-10:00	Registration, check in
10:00-10:05	Introduction to Workshop–Richard Leahy, USA
10:05-10:35	SEEG and the Human Brain Project-Philippe Ryvlin, Switzerland
10:35-11:05	BioPhysics of SEEG-John Mosher, USA
11:05-11:35	Source Localization on Brainstorm-Manish Shah, USA
11:35-12:05	SEEG and Multimodality Clinical Applications in Brainstorm–Jay Gavalla, USA
12:05-13:15	Lunch Break
12:30-13:15	Onsite assistance in installing the material for the training session-Takfarinas Medani & Raymundo Cassani
13:15-13:45	Lecture: Brainstorm overview-Sylvain Baillet, Canada Software structure, typical data workflow Presentation of the example dataset (BIDS-iEEG)
13:45-14:65	Tutorial – Hands-On Brainstorm
13:45-14:45	Anatomy Database explorer MRI volumes, surfaces Anatomical parcellations Coregistration of pre- and post-implantation images
14:45-15:45	SEEG recordings Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image Anatomical labeling of SEEG contacts
15:45-16:45	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 Brainstorm users

End of the workshop, main conference begins at 6pm

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 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.

Troubleshooting

For any technical problem, please contact Takfarinas Medani( medani@usc.edu ) or Raymundo Cassani ( raymundo.cassani@mcgill.ca )

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-<<HTML(<img align="right" alt="archildrens.png" class="attachment" src="/brainstorm/WorkshopArkansas2024?action=AttachFile&do=get&target=archildrens.png" title="archildrens_logo.png" style="width: 45%;">)>>
+<<HTML(<img align="right" alt="ParkCityConference" class="attachment" src="/brainstorm/WorkshopParkCity2024?action=AttachFile&do=get&target=park_city_logo.png" title="park_city_logo.png" style="width: 50%;">)>>
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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.
+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 Park City]]. 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.
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-<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>April 1st, 2024, 9:00-17:00<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>April 1st, 2024, 8:30-17:00<<HTML(</TD></TR>)>>
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-<<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>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://www.aiepilepsy-neuro.com/register.aspx?e=1658&culture=en-US|Please visit this page]]. <<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>[[https://www.archildrens.org/research/researchers/diana-escalona-vargas|Diana Escalona-Vargas]]<<BR>> (Arkansas Children's Hospital, USA)<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>'''  '''[[https://www.aiepilepsy-neuro.com/|AI EPILEPSY 2024]] <<BR>> <<HTML(</TD></TR>)>>
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-<<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>)>>'''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>)>>
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-<<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>-->)>>
+<<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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-TBD
+'''TBD'''
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-=== Day 1 ===
+=== April 1st ===
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-<<HTML(<TR><TD>)>>08:30-09:00<<HTML(</TD><TD>)>> Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>> 09:30-10:00<<HTML(</TD><TD>)>>
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-<<HTML(<TR><TD>)>>09:00-10:00<<HTML(</TD><TD>)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<<HTML(</TD></TR>)>>
+Registration, check in<<HTML(</TD></TR>)>>
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-<<HTML(<TR><TD>)>>10:00-11:00<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''
+<<HTML(<TR><TD>)>>10:00-10:05<<HTML(</TD><TD>)>>
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-Brainstorm database
+Introduction to Workshop–'''Richard Leahy''', USA<<HTML(</TD></TR>)>>
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-Set anatomy
+<<HTML(<TR><TD>)>>10:05-10:35<<HTML(</TD><TD>)>>
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-Review RAW recordings
+SEEG and the Human Brain Project-'''Philippe Ryvlin''', Switzerland<<HTML(</TD></TR>)>>
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-Events
+<<HTML(<TR><TD>)>>10:35-11:05<<HTML(</TD><TD>)>>

BioPhysics of SEEG-'''John Mosher''', USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>11:05-11:35<<HTML(</TD><TD>)>>

Source Localization on Brainstorm-'''Manish Shah''', USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>11:35-12:05<<HTML(</TD><TD>)>>

SEEG and Multimodality Clinical Applications in Brainstorm–'''Jay Gavalla''', USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>12:05-13:15<<HTML(</TD><TD>)>>

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

<<HTML(<TR><TD>)>>12:30-13:15<<HTML(</TD><TD>)>>

Onsite assistance in installing the material for the training session'''-Takfarinas Medani & Raymundo Cassani'''
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-<<HTML(<TR><TD>)>>11:00-12:00<<HTML(</TD><TD>)>>'''Pre-processing'''
+<<HTML(<TR><TD>)>>13:15-13:45<<HTML(</TD><TD>)>>
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-Frequency filters
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-Artifact detection
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-Artifact correction with SSP
+Lecture: Brainstorm overview'''-Sylvain Baillet''', Canada

Software structure, typical data workflow

Presentation of the example dataset (BIDS-iEEG)
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-<<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>13:45-14:65<<HTML(</TD><TD>)>>
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-<<HTML(<TR><TD>)>>13:00-14:30<<HTML(</TD><TD>)>>'''Events and epoching'''
+[[https://neuroimage.usc.edu/brainstorm/WorkshopLA2023|Tutorial – Hands-On Brainstorm]]
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-Events functions
+<<HTML(<TR><TD>)>>13:45-14:45<<HTML(</TD><TD>)>>
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-Import epochs and sensor averages
+'''Anatomy'''

Database explorer

MRI volumes, surfaces

Anatomical parcellations

Coregistration of pre- and post-implantation images
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-<<HTML(<TR><TD>)>>14:30-15:00<<HTML(</TD><TD>)>> '''Spectral and time-frequency analysis of MEG/EEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>14:45-15:45<<HTML(</TD><TD>)>>
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-<<HTML(<TR><TD>)>>15:00-16:30<<HTML(</TD><TD>)>>'''Time-frequency analysis'''
+'''SEEG recordings'''
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-Time-frequency representation of EEG/MEG signals
+Reviewing continuous SEEG recordings

Montages and management of event markers

Marking SEEG contacts on post-implantation image

Anatomical labeling of SEEG contacts

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:45-16:45<<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 Brainstorm users
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-=== Day 2 ===
<<HTML(<TABLE>)>>

<<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

<<HTML(</TD></TR>)>>

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

Statistics, sensor space

Statistics, source space

<<HTML(</TD></TR>)>>

<<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

<<HTML(</TD></TR>)>>

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

Preparing sensor, time-frequency and sources data

<<HTML(</TD></TR>)>>

<<HTML(</TABLE>)>>

=== Day 3 ===
<<HTML(<TABLE>)>>

<<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

<<HTML(</TD></TR>)>>

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

Scripting

GitHub

<<HTML(</TD></TR>)>>

<<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'''

<<HTML(</TABLE>)>>
+End of the workshop, main conference begins at 6pm
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-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 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.
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+For any technical problem, please contact Takfarinas Medani( [[mailto:raymundo.cassani@mcgill.ca|medani@usc.edu]] ) or Raymundo Cassani ( raymundo.cassani@mcgill.ca )

Software

Users

Development