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| = Breckenridge, Colorado, USA: March 3rd, 2025 = | = Breckenridge, Colorado, USA: Monday, March 3rd, 2025 = |
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| <<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/RaymundoCassani|Raymundo Cassani]] <<BR>> (UTH/USC USA, McGill Canada )<<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>)>> |
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| <<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>)>> | <<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: XX <<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> Intro slides | Walkthrough | Survey<<HTML(</TD></TR>)>> | <<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>)>> |
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| {{{#!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. }}} |
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| == Workshop dataset (TBA) == | == Workshop dataset == |
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| == Program (TBD) == | 1. '''raw data''' is located in the file '''`WorkshopBreckenridge_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 '''`WorkshopBreckenridge_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/WorkshopBreckenridge_raw.zip|WorkshopBreckenridge_raw.zip]] 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`WorkshopBreckenridge_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|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 == Program == === Monday, March 3, 2025 === |
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| <<HTML(<TR><TD>)>> 08:30-08:55<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>> 08:30-08:55 <<HTML(</TD><TD>)>> |
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| '''Introduction to the Workshop - '''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> | '''Introduction to the Workshop - '''John Mosher, USC, USA<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>09:00-09:20<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:00-09:30<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>09:20-09:40<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:30-09:45<<HTML(</TD><TD>)>> |
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| '''Presentation - ''' Speaker, institute, Country<<HTML(</TD></TR>)>> | '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]] - '''Yash Vakilna , UTH, USA<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>09:40-10:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:45-09:55<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]] - '''Anand Joshi , UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:55-10:25<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>10:00-10:15<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:25-10:30<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>10:15-11:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:30-11:00<<HTML(</TD><TD>)>> |
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| '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani | '''Tutorial – Hands-On Brainstorm 1/4 - ''' Y.Vakilna, C.Chinara, J.Hampson & T.Medani |
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| ''' Introduction to Brainstorm Interface: Anatomy ''' | ''' Introduction to Brainstorm Interface: Anatomy Data ''' |
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| <<HTML(</TD></TR>)>> |
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| '''Tutorial – Hands-On Brainstorm 2/3 - '''Y.Vakilna, C.Chinara, & T.Medani | '''Tutorial – Hands-On Brainstorm 2/4 - ''' Y.Vakilna, C.Chinara, J.Hampson & T.Medani |
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| ''' Introduction to Brainstorm Interface: sEEG Analysis''' | ''' 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 |
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| Marking SEEG contacts on post-implantation image Anatomical labeling of SEEG contacts Automatic SEEG contacts localization and labeling |
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| '''Lunch Break (Provided? to confirm??)'''<<HTML(</TD></TR>)>> | '''Lunch Break (Not Provided - Please check options [[https://neuroimage.usc.edu/resources/bst_workshop/2025_colorado/breckenridge_conf_map.pdf|here]])'''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>13:00-15:00<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 3/3 - '''Y.Vakilna, C.Chinara, & T.Medani | <<HTML(<TR><TD>)>>13:00-15:00<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 3/4 - ''' Y.Vakilna, C.Chinara, J.Hampson & T.Medani |
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| '''SEEG Analysis''' Import precomputed Brainstorm protocol |
'''SEEG: Analysis''' ==>Import precomputed Brainstorm protocol<== |
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| Compute Forward Model (aka Head Model) Compute Noise Covariance Matrix Compute Inverse Model View Source Modeling Results |
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 |
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| <<HTML(<TR><TD>)>>15:15-17:30<<HTML(</TD><TD>)>> '''SEEG Advanced Analysis''' Modeling interictal spikes Modeling ictal wave Modeling ictal onset with LVFA at Sensor Space Modeling ictal onset with LVFA at Source Space Modeling ictal onset with repetitive spiking at Sensor and Source spaces |
<<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 interictal spikes Modeling ictal wave within the seizure window 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 Pre- / post-MRI volume resection delineation [TODO] |
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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 [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Walkthrough_lax_workshop_2024_v0.pdf|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)'''. End of the workshop, the main conference begins at 6 pm |
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)'''. |
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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 data that you would be interested in processing with Brainstorm. We may ask that you pair with other attendees, for logistics purposes. | 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. |
Breckenridge, Colorado, USA: Monday, March 3rd, 2025
Full-day of lectures and a workshop on Brainstorm as part of the International Conference on 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
| Where | Breckenridge |
| When | March 3rd, 2025, 8:30-17:45 |
| Registration | Please visit this page. |
| Organizers | AI EPILEPSY 2025 |
| Instructors | John Mosher, Takfarinas Medani, Yash Vakilna, Johnson Hampson and Chinmay Chinara (UTH/USC USA) |
| 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 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:
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 WorkshopBreckenridge_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:
- 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 WorkshopBreckenridge_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:
Unzip the downloaded raw data on your desktop: it will create a new folder named WorkshopBreckenridge_raw
Download the pre-processed data. 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)
WorkshopBreckenridge_raw.zip: Raw data, for SEEG localization demonstration
WorkshopBreckenridge_precomputed.zip: Pre-processed Brainstorm protocol for workshop session
Program
Monday, March 3, 2025
| 08:30-08:55 | Registration & Check in |
| 08:55-09:00 | Introduction to the Workshop - John Mosher, USC, USA |
| 09:00-09:30 | BioPhysics of SEEG - John Mosher, UTH, USA |
| 09:30-09:45 | BioPhysics of SEEG - Yash Vakilna , UTH, USA |
| 09:45-09:55 | BioPhysics of SEEG - Anand Joshi , UTH, USA |
| 09:55-10:25 | Brainstorm Overview - Takfarinas Medani, USC, USA |
| 10:25-10:30 | Coffee Break |
| 10:30-11:00 | 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 |
| 11:00-12:15 | 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 |
| 12:15-13:00 | Lunch Break (Not Provided - Please check options here) |
| 13:00-15:00 | Tutorial – Hands-On Brainstorm 3/4 - Y.Vakilna, C.Chinara, J.Hampson & T.Medani 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 |
| 15:00-15:15 | Coffee Break |
| 15:15-17:30 | Tutorial – Hands-On Brainstorm 4/4 - Y.Vakilna, C.Chinara, J.Hampson & T.Medani SEEG: Advanced Analysis Modeling interictal spikes Modeling ictal wave within the seizure window 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 Pre- / post-MRI volume resection delineation [TODO] |
| 17:30 | End of the workshop, main conference begins at 6pm |
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 )