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| <<HTML(<TR><TD>)>>8:30-9:00<<HTML(</TD><TD>)>>Registration<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>> 09:30-10:00<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>9:00-9:30<<HTML(</TD><TD>)>>Onsite assistance in installing the material for the training session <<HTML(</TD></TR>)>> | '''Registration, check in'''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>9:30-10:00<<HTML(</TD><TD>)>>Introduction to Brainstorm (lecture)<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>10:00-10:05<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>10:00-11:00<<HTML(</TD><TD>)>>'''Loading anatomy and recordings''' | '''Introduction to Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> |
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| Database explorer MRI volumes, surfaces Coregistration of pre- and post-implantation images Anatomical parcellations Review RAW recordings Import events |
<<HTML(<TR><TD>)>>10:05-10:35<<HTML(</TD><TD>)>> |
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| '''SEEG and the Human Brain Project-'''Philippe Ryvlin, CHUV, Switzerland<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>10:35-11:05<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]]-'''John Mosher, UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>11:05-11:15<<HTML(</TD><TD>)>> '''Coffee Break'''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>11:15-11:30<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]]'''-Sylvain Baillet, McGill, Canada <<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]]'''-Manish Shah, UTH, USA<<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>)>> |
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| Frequency filters | '''Tutorial – Hands-On Brainstorm - '''Y.Vakilna, J.Hampson, T.Medani & R.Cassani |
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| Artifact correction with ICA/SSP <<HTML(</TD></TR>)>> | '''Anatomy''' |
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| <<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch'' ''break''<<HTML(</TD></TR>)>> | Database explorer MRI volumes, surfaces Anatomical parcellations Coregistration of pre- and post-implantation images |
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| <<HTML(<TR><TD>)>>13:00-13:30<<HTML(</TD><TD>)>>'''Analysis sensor level''' | <<HTML(<TR><TD>)>>14:45-15:30<<HTML(</TD><TD>)>> |
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| Import recordings | '''SEEG recordings''' |
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| Review trials | Reviewing continuous SEEG recordings |
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| Trial averages | Montages and management of event markers Marking SEEG contacts on post-implantation image Anatomical labeling of SEEG contacts |
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| Source estimation (from EEG and MEG recordings) | '''Advanced topics - Based on participants' requests''' |
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| <<HTML(</TD></TR>)>> | Time-frequency analysis: Identification of ictal HFO frequency bands |
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| <<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch'' ''break''<<HTML(</TD></TR>)>> | Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways |
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| <<HTML(<TR><TD>)>>14:30-15:30<<HTML(</TD><TD>)>>'''Analysis source level''' | FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling |
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| Cortex parcellations: Atlases and Scouts | Open discussion with Brainstorm users |
Los Angeles, CA, USA: December 5th, 2024
Full-day workshop, prior of the AES2023 Meeting.
This session will be an introduction to Brainstorm for iEEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops.
General information
| Where | University of Southern California |
| When | Thursdya December 5th, 2024, 8:30-17:30 |
| Instructor | Brainstrom team |
| Audience | Users interested in analyzing iEEG recordings using Brainstorm. Teaching in English. |
| Documents | Introduction 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 WorkshopXXX_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 WorkshopXXX_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:
- TBD
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:
- TBD
- 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)
workshopXXX_raw: Raw data, for SEEG localization demonstration
WorkshopXXX_precomputed.zip: Pre-processed Brainstorm protocol for workshop session
Program (TBD)
| 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 |
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.
Troubleshooting
For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )