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| <<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%;">)>> | <<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%;">)>> |
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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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| == Workshop dataset == | == Workshop dataset (TBA) == |
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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: 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 '''`WorkshopUTAH_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''': . XXXX 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopUTAH_raw`''' 1. Download the '''pre-processed data'''. Do not unzip this file: . XXX 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) * '''`workshopUTAH_raw`''': Raw data, for SEEG localization demonstration * '''`WorkshopUTAH_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session == Program == === April 1st === |
== Program (TBA) == |
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| <<HTML(<TR><TD>)>> 09:30-10:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>> 08:30-9:00<<HTML(</TD><TD>)>> |
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| '''Introduction to Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> | '''Introduction to Workshop–'''<<HTML(</TD></TR>)>> |
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| '''XXXX-'''YYYY, ZZZZ, XZXZ<<HTML(</TD></TR>)>> | '''Brainstorm Overview & Hands-On '''- '''Brainstorm team''' |
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| '''XXXXX-YYYY''', UTH, USA<<HTML(</TD></TR>)>> | '''Lunch Break '''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>11:05-11:15<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>10:00-10:15<<HTML(</TD><TD>)>> |
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| '''Coffee Break'''<<HTML(</TD></TR>)>> | '''Coffee Break<<BR>>'''Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>> |
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| '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]]'''-XXXX, YYYY, ZZZZ | '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani |
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| <<HTML(<TR><TD>)>>11:30-12:00<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/ManishShah_slides.pdf|Source Localization on Brainstorm]]'''-XXXXX, YYYY, ZZZ<<HTML(</TD></TR>)>> <<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''' |
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| MRI volumes, surfaces | Loading anatomy and recordings |
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| Anatomical parcellations | Review MRI volumes, surfaces, Anatomical parcellations |
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| Coregistration of pre- and post-implantation images | Review raw data, event markers, EEG/MEG sensors |
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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''' | '''EEG and MEG Analysis''' 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 <<HTML(<TR><TD>)>>12:15-13:00<<HTML(</TD><TD>)>> '''Lunch Break (Provided)'''<<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 '''SEEG Analysis''' |
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| Anatomical labeling of SEEG contacts |
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| '''Advanced topics - Based on participants' requests''' | '''Advanced topics - SEEG Analsysis''' |
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| FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling Open discussion with Brainstorm users |
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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)'''. |
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| For any technical problem, please contact Takfarinas Medani ( medani@usc.edu ) |
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 a 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 (TBA)
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 (TBA)
| 08:30-9:00 | Registration, check in |
| 09:00-09:05 | Introduction to Workshop– |
| 09:05-12:15 | Brainstorm Overview & Hands-On - Brainstorm team |
| 12:15-13:00 | Lunch Break |
| 10:00-10:15 | Coffee Break |
| 10:15-10:45 | Tutorial – Hands-On Brainstorm 1/3 - Y.Vakilna, C.Chinara, & T.Medani Introduction to Brainstorm Interface Database explorer Loading anatomy and recordings Review MRI volumes, surfaces, Anatomical parcellations Review raw data, event markers, EEG/MEG sensors |
| 10:45-12:15 | Tutorial – Hands-On Brainstorm 2/3 - Y.Vakilna, C.Chinara, & T.Medani EEG and MEG Analysis 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 |
| 12:15-13:00 | Lunch Break (Provided) |
| 13:00-15:00 | Tutorial – Hands-On Brainstorm 3/3 - Y.Vakilna, C.Chinara, & T.Medani SEEG Analysis Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image |
| 15:00-15:15 | Coffee Break |
| 15:15-17:00 | Advanced topics - SEEG Analsysis Time-frequency analysis: Identification of ictal HFO frequency bands Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways |
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, 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 )