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| 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 Breckenridge]]. This session will be a hands-on Brainstorm features for sEEG analysis. | 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 Breckenridge]]. This session will be hands-on Brainstorm features for sEEG analysis. |
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| <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>March 3rd, 2025, 8:30-17:00<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>March 3rd, 2025, 8:30-17:45<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>''' '''[[https://www.aiepilepsy-neuro.com/|AI EPILEPSY 2024]] <<BR>> <<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>''' '''[[https://www.aiepilepsy-neuro.com/|AI EPILEPSY 2025]] <<BR>> <<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 | Walkthrough | [[https://docs.google.com/forms/d/e/1FAIpQLSfLM_V2LISKa-ZPKUqrh6s4ezWFbpnUIBuLyIC1Tehw7GjZdw/viewform?usp=sf_link|Survey]]<<HTML(</TD></TR>)>> |
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| 1. '''raw data''' is located in the file '''`XXXX.zip`''' which contains raw SEEG recordings (in EDF format), T1 MRI and CT scan (both in NIfTI format). The raw SEEG recordings correspond to: | 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: |
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| 1. '''pre-processed data''' is located in the file '''`WorkshopUTAH_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed. | 1. '''pre-processed data''' is located in the file '''`workshopColorado_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed. |
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| . XXXX 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopUTAH_raw`''' |
. [[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`''' |
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| . XXX | . [[https://box.bic.mni.mcgill.ca/s/Yqjt3sciljtHMqF|workshopColorado_precomputed.zip]] |
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| * '''`workshopUTAH_raw`''': Raw data, for SEEG localization demonstration * '''`WorkshopUTAH_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session |
* '''`workshopColorado_raw.zip`''': Raw data, for SEEG localization demonstration * '''`workshopColorado_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session |
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| === April 1st === | === March 3rd === |
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| <<HTML(<TR><TD>)>> 09:30-10:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>> 08:30-08:55 <<HTML(</TD><TD>)>> |
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| '''Registration, check in'''<<HTML(</TD></TR>)>> | '''Registration & Check in'''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>10:00-10:05<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>08:55-09:00<<HTML(</TD><TD>)>> |
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| '''Introduction to Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> | '''Introduction to the Workshop - '''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>10:05-10:35<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:00-09:20<<HTML(</TD><TD>)>> |
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| '''XXXX-'''YYYY, ZZZZ, XZXZ<<HTML(</TD></TR>)>> | '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]] - '''John Mosher, UTH, USA<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>10:35-11:05<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:20-09:40<<HTML(</TD><TD>)>> |
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| '''XXXXX-YYYY''', UTH, USA<<HTML(</TD></TR>)>> | '''Presentation - ''' Speaker, institute, Country<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>11:05-11:15<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:40-10:00<<HTML(</TD><TD>)>> |
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| '''Coffee Break'''<<HTML(</TD></TR>)>> | '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]] '''- Takfarinas Medani, USC, USA<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>11:15-11:30<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:00-10:15<<HTML(</TD><TD>)>> |
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| '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]]'''-XXXX, YYYY, ZZZZ | '''Coffee Break<<BR>>'''Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>11:30-12:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:15-11:00<<HTML(</TD><TD>)>> |
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| '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/ManishShah_slides.pdf|Source Localization on Brainstorm]]'''-XXXXX, YYYY, ZZZ<<HTML(</TD></TR>)>> | '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani (Add Johnson) |
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| <<HTML(<TR><TD>)>>12:00-12:30<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JayGavvala_slides.pdf|SEEG and Multimodality Clinical Applications in Brainstorm]]'''–Jay Gavvala, UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:30-13:15<<HTML(</TD><TD>)>> '''Lunch Break (Not Provided)'''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:45-13:15<<HTML(</TD><TD>)>> Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>> <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>13:15-16:45<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm - '''Y.Vakilna, J.Hampson, T.Medani & R.Cassani <<HTML(<TR><TD>)>>13:15-14:45<<HTML(</TD><TD>)>> '''Anatomy''' |
''' Introduction to Brainstorm Interface: Anatomy Data ''' |
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| Coregistration of pre- and post-implantation images | CT volumes Coregistration: pre- / post-implantation images <<HTML(</TD></TR>)>> |
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| <<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>11:00-12:15<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>14:45-15:30<<HTML(</TD><TD>)>> | '''Tutorial – Hands-On Brainstorm 2/3 - '''Y.Vakilna, C.Chinara, & T.Medani |
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| '''SEEG recordings''' | ''' Introduction to Brainstorm Interface: Functional Data: sEEG ''' '''(We recommend you bring a mouse for this section)''' 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 | <<HTML(<TR><TD>)>>12:15-13:00<<HTML(</TD><TD>)>> |
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| Anatomical labeling of SEEG contacts | '''Lunch Break (Provided? to confirm/ ask one of the sponsor sEEG??)'''<<HTML(</TD></TR>)>> |
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| <<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>13:00-15:00<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 3/3 - '''Y.Vakilna, C.Chinara, & T.Medani |
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| <<HTML(<TR><TD>)>>15:30-15:45<<HTML(</TD><TD>)>> | '''SEEG Analysis''' |
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| '''Coffee Break'''<<HTML(</TD></TR>)>> | ==>Import precomputed Brainstorm protocol<== |
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| <<HTML(<TR><TD>)>>15:45-16:45<<HTML(</TD><TD>)>> | sEEG Montage Configuration |
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| '''Advanced topics - Based on participants' requests''' | sEEG Frequency Analysis and Filtering |
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| Time-frequency analysis: Identification of ictal HFO frequency bands | Compute Forward Model (aka Head Model) |
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| Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways | Compute Noise Covariance Matrix |
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| FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling | Compute Inverse Model |
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| Open discussion with Brainstorm users | View Source Results Atlases and Scouts <<HTML(<TR><TD>)>>15:00-15:15<<HTML(</TD><TD>)>> '''Coffee Break (provided)'''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>15:15-17:30<<HTML(</TD><TD>)>> '''SEEG Advanced Analysis''' Modeling interictal spikes Modeling ictal wave within the seizure window 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 |
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| End of the workshop, main conference begins at 6pm | 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 |
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| For any technical problem, please contact Takfarinas Medani ( medani@usc.edu ) & Chinmay ... Todo |
Breckenridge, Colorado, USA: 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 Raymundo Cassani (UTH/USC USA, McGill Canada ) |
| 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 | 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.
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 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:
- 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 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.
Download the raw data:
Unzip the downloaded raw data on your desktop: it will create a new folder named workshopColorado_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)
workshopColorado_raw.zip: Raw data, for SEEG localization demonstration
workshopColorado_precomputed.zip: Pre-processed Brainstorm protocol for workshop session
Program
March 3rd
| 08:30-08:55 | Registration & Check in |
| 08:55-09:00 | Introduction to the Workshop - Richard Leahy, USC, USA |
| 09:00-09:20 | BioPhysics of SEEG - John Mosher, UTH, USA |
| 09:20-09:40 | Presentation - Speaker, institute, Country |
| 09:40-10:00 | Brainstorm Overview - Takfarinas Medani, USC, USA |
| 10:00-10:15 | Coffee Break |
| 10:15-11:00 | Tutorial – Hands-On Brainstorm 1/3 - Y.Vakilna, C.Chinara, & T.Medani (Add Johnson) 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 2/3 - Y.Vakilna, C.Chinara, & T.Medani Introduction to Brainstorm Interface: Functional Data: sEEG (We recommend you bring a mouse for this section) 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 (Provided? to confirm/ ask one of the sponsor sEEG??) |
| 13:00-15:00 | Tutorial – Hands-On Brainstorm 3/3 - Y.Vakilna, C.Chinara, & T.Medani SEEG Analysis ==>Import precomputed Brainstorm protocol<== sEEG Montage Configuration sEEG Frequency Analysis and Filtering Compute Forward Model (aka Head Model) Compute Noise Covariance Matrix Compute Inverse Model View Source Results Atlases and Scouts |
| 15:00-15:15 | Coffee Break (provided) |
| 15:15-17:30 | SEEG Advanced Analysis Modeling interictal spikes Modeling ictal wave within the seizure window 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 |
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).
End of the workshop, the main conference begins at 6 pm
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 ) & Chinmay ... Todo