= Los Angeles, CA, USA: December 5th, 2024 = = Register Now: seats are very limited! = <)>> This full-day workshop will take place at the [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]] on Dec 5th, immediately prior to the American Epilepsy Society Meeting ([[https://aesnet.org/AES-annual-meeting|AES 2024)]]. This session will highlight Brainstorm's unique features for multimodal scalp electrophysiology data analysis (EEG/MEG), with a second focus on intracranial recordings (iEEG). Participants are invited to their personal laptops for a unique hands-on experience (data will be provided). Registration is now open via this [[https://my.cheddarup.com/c/brainstormworkshopla2024/items?cart|page]]. == General information == <)>> <)>>'''Where'''<)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]]<)>> <)>>'''When'''<)>>Thursday December 5th, 2024, 8:30-17:30<)>> <)>>'''Instructor'''<)>>Brainstorm team<)>> <)>>'''Registration'''<)>> [[https://my.cheddarup.com/c/brainstormworkshopla2024/items?cart|Registration is now open]]. <)>> <)>>'''Audience'''''' '''<)>>Users interested in analyzing iEEG recordings using Brainstorm.<
>Teaching in English. <)>> <)>>'''Documents'''<)>> [[https://box.bic.mni.mcgill.ca/s/XRahw8lOSpgFetj|Introduction slides]] | [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Walkthrough_lax_workshop_2024_v0.pdf|Walkthrough]] |[[https://forms.gle/JfafQxq4NPnDKdGaA|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. {{{#!wiki tip We highly recommend bringing an '''external mouse''' on the day of the workshop. Most of the manipulations are done with the mouse, and some involve an intense use of the scrolling operation. }}} == 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 multimodal data. In the morning session we will work on combined EEG/MEG data sets. In the afternoon we will use SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston. === Morning Session (EEG and MEG Analysis) === The workshop dataset for this session is a pre-processed version of the dataset used in the [[Tutorials/Yokogawa|Brainstorm tutorial on median nerve stimulation]]. It consists of simultaneous EEG and MEG recordings during a median nerve stimulation experiment (right arm). A full description of the dataset can be found [[Tutorials/Yokogawa#Description_of_the_experiment|here]]. Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop. 1. Download the tutorial dataset (360 MB): . [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Data/workshopLaxMorning.zip|workshopLaxMorning.zip]] 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshopLaxMorning`''' 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) * '''`workshopLaxMorning.zip`''': Dataset used during the workshop session === Afternoon Session (SEEG Analysis) === In this session of the 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 '''`workshopLaxAfternoon_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 '''`workshopLaxAfternoon_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''': . [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Data/workshopLaxAfternoon_raw.zip|workshopLaxAfternoon_raw.zip]] 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopLaxAfternoon_raw`''' 1. Download the '''pre-processed data'''. Do not unzip this file: . [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Data/workshopLaxAfternoon_precomputed.zip|workshopLaxAfternoon_precomputed.zip]] 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) * '''`workshopLaxAfternoon_raw.zip`''': Raw data, for SEEG localization demonstration * '''`workshopLaxAfternoon_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session == Program == === Thursday, December 5, 2024 === <)>> <)>> 08:30-09:00<)>> '''Registration & Check in'''<)>> <)>>09:00-09:05<)>> '''Introduction to the Workshop - '''Richard Leahy, USC, USA<)>> <)>>09:05-09:35<)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of MEG/EEG/SEEG]] - '''John Mosher, UTH, USA<)>> <)>>09:35-10:00<)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]] '''- Takfarinas Medani, USC, USA<)>> <)>>10:00-10:15<)>> '''Coffee Break<
>'''Onsite assistance in installing the material for the training session<)>> <)>>10:15-10:45<)>> '''Tutorial – Hands-On Brainstorm 1/5 - '''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 2/5 - '''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)'''<)>> <)>>13:00-14:00<)>> '''Tutorial – Hands-On Brainstorm 3/5 - '''Y.Vakilna, C.Chinara, & T.Medani '''SEEG: Anatomy Data''' CT volumes Coregistration: pre- / post-implantation images '''SEEG: Functional Data''' 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 <)>> <)>>14:00-15:30<)>> '''Tutorial – Hands-On Brainstorm 4/5 - '''Y.Vakilna, C.Chinara, & T.Medani '''SEEG Analysis''' ==>Import precomputed Brainstorm protocol<== sEEG Montage Configuration sEEG Frequency Analysis and Filtering Compute Forward Model (aka the Head or Lead Field Model) Compute Noise Covariance Matrix Compute Inverse Model View Source Results Atlases and Scouts <)>> <)>>15:30-15:45<)>> '''Coffee Break'''<)>> <)>>15:45-17:00<)>> '''Tutorial – Hands-On Brainstorm 5/5 - '''Y.Vakilna, C.Chinara, & T.Medani '''Advanced topics - SEEG Analysis''' Modeling interictal spikes Modeling ictal wave within the seizure window <)>> <)>>17:00<)>> '''End of the workshop''' <)>> <)>> 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)'''. == Troubleshooting == For any technical problem, please contact Takfarinas Medani ( medani@usc.edu )