)>>'''Where'''<)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]]<)>>
<)>>'''When'''<)>>Thursdya December 5th, 2024, 8:30-17:30<)>>
<)>>'''Instructor'''<)>>Brainstrom team<)>>
<)>>'''Registration'''<)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#registration|T]]BD. <-->)>>
<)>>'''Audience'''''' '''<)>>Users interested in analyzing iEEG recordings using Brainstorm.<
>Teaching in English. <)>>
<)>>'''Documents'''<)>> [[https://box.bic.mni.mcgill.ca/s/XRahw8lOSpgFetj|Introduction slides]] | [[https://box.bic.mni.mcgill.ca/s/rpkrUdfXUSxjArh|Walkthrough]] | [[https://forms.gle/R4g5w1A3aUNz8jMB9|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: <
>[[WorkshopGeneralInstall|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.
1. '''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:
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 '''`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.
1. Download the '''raw data''':
. TBD
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:
. TBD
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)
* '''`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<)>>
'''XXXX-'''XXXX, XXXX<)>>
<)>>10:35-11:05<)>>
'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]]-'''John Mosher, UTH, USA<)>>
<)>>11:05-11:15<)>>
'''Coffee Break'''<)>>
<)>>11:15-11:30<)>>
'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]]'''-Sylvain Baillet, McGill, Canada
<)>>11:30-12:00<)>>
'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/ManishShah_slides.pdf|Source Localization on Brainstorm]]'''-Manish Shah, UTH, USA<)>>
<)>>12:00-12:30<)>>
'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JayGavvala_slides.pdf|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 [[https://box.bic.mni.mcgill.ca/s/rpkrUdfXUSxjArh|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 [[https://box.bic.mni.mcgill.ca/s/kYKqad5wzYabzq1|this script]].
== Troubleshooting ==
For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )
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