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| = Toulouse, France: Monday, March 3rd, 2025 = | = Toulouse, France: Wednesday, March 19th, 2025 = <<HTML(<img align="right" alt="ToulouseConference" class="attachment" src="/brainstorm/WorkshopToulouse2025?action=AttachFile&do=get&target=micmiac2025.png" title="Toulouse_logo.png" style="width: 50%;">)>> |
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| <<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%;">)>> 2*2 hours of lectures and a workshop on Brainstorm as part of the MicMac 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. https://micmac-workshop.org/ a scientific event focused on intracranial electrophysiological recordings using micro- and macro-electrodes. Participants will learn how to use Brainstorm and access its new tools on their personal laptops. |
A 4-hour session, including lectures and a hands-on workshop on Brainstorm, will be featured as part of the [[https://micmac-workshop.org/|MicMac Conference in Toulouse, France]]. This scientific event focuses on intracranial electrophysiological recordings using micro- and macro-electrodes. The hands-on session will explore Brainstorm's features for sEEG analysis, allowing participants to learn how to use the software effectively. Attendees will also gain access to Brainstorm's new tools and practice using them on their personal laptops. |
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| <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> Toulouse, France<<HTML(</TD></TR>)>> | |
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| <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>March 19th, 2025, 10:30-16:00<<HTML(</TD></TR>)>> | |
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| <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> Breckenridge<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://micmac-workshop.org/register/|Please visit this page]]. <<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>''' '''[[https://micmac-workshop.org/program/|MicMac 2025]] <<BR>> <<HTML(</TD></TR>)>> | |
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<<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>)>>'''Instructors'''<<HTML(</TD><TD>)>> [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani|Takfarinas Medani]], [[https://www.neurotrack.fr/|Anne Sophie Dubarry]] and Maximilien Chaumon<<BR>> <<HTML(</TD></TR>)>> |
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<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> Intro slides | [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Walkthrough_BST_Workshop_Colorado_v0.pdf|Walkthrough]] | [[https://docs.google.com/forms/d/e/1FAIpQLSfLM_V2LISKa-ZPKUqrh6s4ezWFbpnUIBuLyIC1Tehw7GjZdw/viewform?usp=sf_link|Survey]]<<HTML(</TD></TR>)>> |
<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> Intro slides | [[toDo|Walkthrough]] | [[https://forms.gle/QqhoUDDZ9uZ4jv1h9|Survey]]<<HTML(</TD></TR>)>> |
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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. |
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. |
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| 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. |
We highly recommend bringing an '''external mouse''' on the workshop day. Most of the manipulations are done with the mouse, and some involve an intense use of the scrolling operation. |
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| 1. The data is distributed as '''raw''' and '''pre-processed''' data. a. '''raw data''' is located in the file '''`WorkshopSEEG_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 |
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| a. '''pre-processed data''' is located in the file '''`WorkshopSEEG_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed. | |
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| The data is distributed as '''raw''' and '''pre-processed''' data. | 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/Data/WorkshopSEEG_raw.zip|WorkshopSEEG_raw.zip]].<<BR>>Unzip the downloaded raw data on your desktop: it will create a new folder named '''`WorkshopSEEG_raw`''' |
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1. '''raw data''' is located in the file '''`WorkshopColorado_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 '''`workshopColorado_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''': . [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Data/workshopColorado_raw.zip|workshopColorado_raw.zip]] 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopColorado_raw`''' 1. Download the '''pre-processed data'''. Do not unzip this file: . [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Data/workshopColorado_precomputed.zip|workshopColorado_precomputed.zip]] |
a. Download the '''pre-processed data (3.5 GB)'''. Do not unzip this file: * [[https://neuroimage.usc.edu/resources/bst_workshop/Data/WorkshopSEEG_precomputed.zip|WorkshopSEEG_precomputed.zip]] |
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| * '''`brainstorm3`''': the software folder, containing the source code and the compiled executable * '''`brainstorm_db`''': your Brainstorm database (which should be empty for now) * '''`WorkshopSEEG_raw.zip`''': Raw data, for SEEG localization demonstration * '''`WorkshopSEEG_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session |
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| * '''`brainstorm3`''': the software folder, containing the source code and the compiled executable | == 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. |
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| * '''`brainstorm_db`''': your Brainstorm database (which should be empty for now) | {{{#!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. |
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| * '''`workshopColorado_raw.zip`''': Raw data, for SEEG localization demonstration * '''`workshopColorado_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session |
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)]]''' |
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=== Monday, March 3, 2025 === |
=== Wednesday, March 19th, 2025 === |
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| <<HTML(<TR><TD>)>> 09:30-10:00 <<HTML(</TD><TD>)>> | |
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| '''Registration & Breakfast '''<<HTML(</TD></TR>)>> | |
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| <<HTML(<TR><TD>)>> 08:30-08:55 <<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:00-10:45<<HTML(</TD><TD>)>> |
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| '''Lectures: Brainstorm Overview & BioPhysics of SEEG '''<<HTML(</TD></TR>)>> | |
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| <<HTML(<TR><TD>)>>10:45-11:00<<HTML(</TD><TD>)>> | |
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| '''Registration & Check in'''<<HTML(</TD></TR>)>> | '''Workshop Preparation<<BR>>'''Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>> |
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<<HTML(<TR><TD>)>>08:55-09:00<<HTML(</TD><TD>)>> '''Introduction to the Workshop - '''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:00-09:30<<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>)>>09:30-10:00<<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 1/4 - ''' Y.Vakilna, C.Chinara, J.Hampson & T.Medani |
'''Tutorial – Hands-On Brainstorm - ''' |
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| CT/MRI volumes Coregistration <<HTML(</TD></TR>)>> | |
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| <<HTML(<TR><TD>)>>11:45-12:30<<HTML(</TD><TD>)>> | |
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| CT volumes Coregistration: pre- / post-implantation images <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>11:00-12:15<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 2/4 - ''' Y.Vakilna, C.Chinara, J.Hampson & T.Medani |
'''Tutorial – Hands-On Brainstorm - ''' |
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Manual marking of SEEG contacts on post-implantation image Automatic marking of SEEG contacts on post-implantation image |
Manual marking of SEEG contacts on post-implantation CT image |
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| Demo: Automatic marking of SEEG contacts on post-implantation CT/MRI image | |
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<<HTML(<TR><TD>)>>12:15-13:00<<HTML(</TD><TD>)>> |
<<HTML(<TR><TD>)>>12:30-13:30<<HTML(</TD><TD>)>> |
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<<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''' |
<<HTML(<TR><TD>)>>13:30-14:30<<HTML(</TD><TD>)>> '''SEEG: Analysis''' |
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<<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''' |
<<HTML(<TR><TD>)>>14:30-16:00<<HTML(</TD><TD>)>> '''SEEG: Advanced Analysis''' |
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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 |
Modeling ictal onset with LVFA |
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| <<HTML(<TR><TD>)>>16:00<<HTML(</TD><TD>)>> | |
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| End of the workshop & Starting of the [[https://micmac-workshop.org/program/|Main Conference]] | |
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| <<HTML(<TR><TD>)>>17:30<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>16:30-17:30<<HTML(</TD><TD>)>> '''Epileptogenicity index: a tool for ictal SEEG signal analysis''' |
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| ''Speakers – Julia Scholly, Fabrice Bartolomei'' | |
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| <<HTML(<TR><TD>)>>17:30-18:30<<HTML(</TD><TD>)>> | |
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| End of the workshop, main conference begins at 6pm | '''Diving into HFO analyses ''' |
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| ''Speaker – Jonathan Curot'' | |
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| <<HTML(<TR><TD>)>>18:30-19:30<<HTML(</TD><TD>)>> '''The PHRC NenuFaR great debate: clinical usefulness of HFO?''' ''Speakers – Fabrice Bartolomei, Jonathan Curot, Philippe Kahane'' |
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We will provide a [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/Walkthrough_BST_Workshop_Colorado_v0.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)'''. |
We will provide a [[XXXX|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)'''. |
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Toulouse, France: Wednesday, March 19th, 2025
A 4-hour session, including lectures and a hands-on workshop on Brainstorm, will be featured as part of the MicMac Conference in Toulouse, France. This scientific event focuses on intracranial electrophysiological recordings using micro- and macro-electrodes. The hands-on session will explore Brainstorm's features for sEEG analysis, allowing participants to learn how to use the software effectively. Attendees will also gain access to Brainstorm's new tools and practice using them on their personal laptops.
General information
| Where | Toulouse, France |
| When | March 19th, 2025, 10:30-16:00 |
| Registration | Please visit this page. |
| Organizers | MicMac 2025 |
| Instructors | Takfarinas Medani, Anne Sophie Dubarry and Maximilien Chaumon |
| Audience | Users interested in analyzing sEEG recordings using Brainstorm. Some experience with iEEG and signal processing is recommended. Teaching in English. Number of participants: XX |
| Slides | Intro 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.
We highly recommend bringing an external mouse on the workshop day. 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:
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.
raw data is located in the file WorkshopSEEG_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:
- Two files containing seizure onset:
- Seizure onset with Low-voltage-fast-activity
- Seizure with Ictal repetitive spiking
- One file with interictal spike, and
- One file containing baseline recordings
- Two files containing seizure onset:
pre-processed data is located in the file WorkshopSEEG_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.
Download the raw data (512 MB):
WorkshopSEEG_raw.zip.
Unzip the downloaded raw data on your desktop: it will create a new folder named WorkshopSEEG_raw
Download the pre-processed data (3.5 GB). Do not unzip this file:
- 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)
WorkshopSEEG_raw.zip: Raw data, for SEEG localization demonstration
WorkshopSEEG_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.
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.
The prerelease compiled executable with the associated data:
brainstorm_250301_prerelease_bin.zip
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.
Walkthrough video showing features to explore in this prerelease:
Automatic SEEG contact localization and labeling (Brainstorm+GARDEL)
Program
Wednesday, March 19th, 2025
| 09:30-10:00 | Registration & Breakfast |
| 10:00-10:45 | Lectures: Brainstorm Overview & BioPhysics of SEEG |
| 10:45-11:00 | Workshop Preparation |
| 11:00-11:45 | Tutorial – Hands-On Brainstorm - Introduction to Brainstorm Interface: Anatomy Data Database explorer MRI volumes, surfaces Anatomical parcellations CT/MRI volumes Coregistration |
| 11:45-12:30 | Tutorial – Hands-On Brainstorm - Introduction to Brainstorm Interface: sEEG Functional Data. Manual marking of SEEG contacts on post-implantation CT image Automatic anatomical labeling of SEEG contacts Demo: Automatic marking of SEEG contacts on post-implantation CT/MRI image Reviewing continuous SEEG recordings Montages and management of event markers |
| 12:30-13:30 | Lunch Break |
| 13:30-14:30 | SEEG: Analysis ==>Import precomputed Brainstorm protocol<== sEEG Montage Configuration sEEG Frequency Analysis and Filtering Compute Forward Model (aka the Head or Lead Field Model) Compute Noise Covariance Matrix Compute Inverse Model View Source Results Atlases and Scouts |
| 14:30-16:00 | SEEG: Advanced Analysis Modeling interictal spikes Modeling ictal wave within the seizure window Modeling ictal onset with LVFA |
| 16:00 | End of the workshop & Starting of the Main Conference |
| 16:30-17:30 | Epileptogenicity index: a tool for ictal SEEG signal analysis Speakers – Julia Scholly, Fabrice Bartolomei |
| 17:30-18:30 | Diving into HFO analyses Speaker – Jonathan Curot |
| 18:30-19:30 | The PHRC NenuFaR great debate: clinical usefulness of HFO? Speakers – Fabrice Bartolomei, Jonathan Curot, Philippe Kahane |
We will provide 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).
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 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 )