Park City, Utah, USA: April 1st, 2024
Full-day of lectures and a workshop on Brainstorm as part of the International Conference on Artificial Intelligence in Epilepsy and Neurological Disorders in Park City. This session will be an introduction to Brainstorm features for sEEG analysis.
Participants will learn how to use Brainstorm and access its new tools on their personal laptops.
General information
| Where | Park City |
| When | April 1st, 2024, 8:30-17:00 |
| Registration | Please visit this page. |
| Organizers | AI EPILEPSY 2024 |
| 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 WorkshopUTAH_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 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.
Download the raw data:
Unzip the downloaded raw data on your desktop: it will create a new folder named workshopUTAH_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)
workshopUTAH_raw: Raw data, for SEEG localization demonstration
WorkshopUTAH_precomputed.zip: Pre-processed Brainstorm protocol for workshop session
Program
April 1st
| 09:30-10:00 | Registration, check in |
| 10:00-10:05 | Introduction to Workshop–Richard Leahy, USC, USA |
| 10:05-10:35 | SEEG and the Human Brain Project-Philippe Ryvlin, CHUV, Switzerland |
| 10:35-11:05 | BioPhysics of SEEG-John Mosher, UTH, USA |
| 11:05-11:15 | Coffee Break |
| 11:15-11:30 | Brainstorm Overview-Sylvain Baillet, McGill, Canada |
| 11:30-12:00 | Source Localization on Brainstorm-Manish Shah, UTH, USA |
| 12:00-12:30 | SEEG and Multimodality Clinical Applications in Brainstorm–Jay Gavvala, UTH, USA |
| 12:30-13:15 | Lunch Break (Not Provided) |
| 12:45-13:15 | Onsite assistance in installing the material for the training session |
| 13:15-16:45 | Tutorial – Hands-On Brainstorm - Y.Vakilna, J.Hampson, T.Medani & R.Cassani |
| 13:15-14:45 | Anatomy Database explorer MRI volumes, surfaces Anatomical parcellations Coregistration of pre- and post-implantation images |
| 14:45-15:30 | SEEG recordings Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image Anatomical labeling of SEEG contacts |
| 15:30-15:45 | Coffee Break |
| 15:45-16:45 | Advanced topics - Based on participants' requests Time-frequency analysis: Identification of ictal HFO frequency bands Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling Open discussion with Brainstorm users |
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 ) or Raymundo Cassani ( raymundo.cassani@mcgill.ca )
We 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.