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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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| == Workshop dataset (TBA) == | == Workshop dataset == |
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| == Program (TBA) == | == Program == |
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| <<HTML(<TR><TD>)>> 08:30-9:00<<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>)>>09:00-09:05<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>08:55-09:00<<HTML(</TD><TD>)>> |
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| '''Introduction to Workshop–'''<<HTML(</TD></TR>)>> | '''Introduction to the Workshop - '''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>09:05-12:15<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:00-09:20<<HTML(</TD><TD>)>> |
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| '''Brainstorm Overview & Hands-On '''- '''Brainstorm team''' | '''[[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>)>>12:15-13:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>09:20-09:40<<HTML(</TD><TD>)>> |
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| '''Lunch Break '''<<HTML(</TD></TR>)>> | '''Presentation - ''' Speaker, institute, Country<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:40-10:00<<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>)>> |
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| <<HTML(<TR><TD>)>>10:15-10:45<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:15-11:00<<HTML(</TD><TD>)>> |
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| '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani | '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani (Add Johnson) |
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| '''Introduction to Brainstorm Interface''' | ''' Introduction to Brainstorm Interface: Anatomy Data ''' |
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| Loading anatomy and recordings | MRI volumes, surfaces |
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| Review MRI volumes, surfaces, Anatomical parcellations | Anatomical parcellations |
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| Review raw data, event markers, EEG/MEG sensors | CT volumes Coregistration: pre- / post-implantation images <<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>10:45-12:15<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>11:00-12:15<<HTML(</TD><TD>)>> |
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| '''EEG and MEG Analysis''' | ''' Introduction to Brainstorm Interface: Functional Data: sEEG ''' ===> We Recommend you bring a mouse for this section <=== |
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| Review RAW recordings & events Frequency filters Artifact detection & correction '''Analysis sensor level''' Import recordings Review trials Trial averages '''Source estimation''' Forward model (aka Head model) Noise covariance matrix Source estimation |
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 |
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| '''Lunch Break (Provided)'''<<HTML(</TD></TR>)>> | '''Lunch Break (Provided? to confirm/ ask one of the sponsor sEEG??)'''<<HTML(</TD></TR>)>> |
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| '''SEEG Analysis''' Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image <<HTML(</TD></TR>)>> |
'''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 |
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| '''Coffee Break'''<<HTML(</TD></TR>)>> | '''Coffee Break (provided)'''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>15:15-17:00<<HTML(</TD><TD>)>> '''Advanced topics - SEEG Analsysis''' Time-frequency analysis: Identification of ictal HFO frequency bands Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways |
<<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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| 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)'''. | 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)'''. |
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| End of the workshop, main conference begins at 6pm | 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 ) | 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.
Program
| 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