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| 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|AES2024)]]. <<BR>> This session will highlight Brainstorm's unique features for multimodal scalp electrophysiology data analysis (EEG/MEG), with a second focus on intracranial recordings (iEEG). | <<HTML(<img align="right" alt="LA2024_logo" class="attachment" src="/brainstorm/WorkshopLA2024?action=AttachFile&do=get&target=LA2024_logo.png" title="LA2024_logo.png" style="width: 45%;">)>> This full-day workshop will take place at the [[https://maps.app.goo.gl/WK6XLjXALSJEwHd47|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). |
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Registration is now open via this [[https://my.cheddarup.com/c/brainstormworkshopla2024/items?cart|page]]. |
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| <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]]<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://maps.app.goo.gl/WK6XLjXALSJEwHd47|University of Southern California]] (Room EEB-132)<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>Brainstorm team<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://my.cheddarup.com/c/brainstormworkshopla2024/items?cart|Registration is now open]]. <<HTML(</TD></TR>)>> |
<<HTML(<TR><TD>)>>'''Instructors'''<<HTML(</TD><TD>)>>Takfarinas Medani, Yash Vakilna, Chinmay Chinara, Woojae Jeong<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> Registration is now '''closed'''. <<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>> [[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/9MCqaWz5NU8AFTpc8|Survey]]<<HTML(</TD></TR>)>> <<HTML(</TABLE>)>> | <<HTML(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>> [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Intro-Slides-Tak.pdf|Introduction slides]] | [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Walkthrough-Workshop-LosAngeles-2024.docx.pdf|Walkthrough]] |[[https://forms.gle/JfafQxq4NPnDKdGaA|Survey]]<<HTML(</TD></TR>)>> <<HTML(</TABLE>)>> |
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| {{{#!wiki important 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. }}} |
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| In this workshop, we will be working on a multimocal 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. [The detailed data and program will be released asap] |
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 (1.5 GB): . [[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. |
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| 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: | 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: |
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| 1. '''pre-processed data''' is located in the file '''`WorkshopXXX_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed. | 1. '''pre-processed data''' is located in the file '''`workshopLaxAfternoon_precomputed.zip`''', which contains a Brainstorm protocol with the raw data already pre-processed. |
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| 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. Download the '''raw data '''(500 MB): . [[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 '''(3 GB). Do not unzip this file: . [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Data/workshopLaxAfternoon_precomputed.zip|workshopLaxAfternoon_precomputed.zip]] |
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| * '''`workshopXXX_raw`''': Raw data, for SEEG localization demonstration * '''`WorkshopXXX_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session == Program (TBD) == |
* '''`workshopLaxAfternoon_raw.zip`''': Raw data, for SEEG localization demonstration * '''`workshopLaxAfternoon_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session == Program == === Thursday, December 5, 2024 === |
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| <<HTML(<TR><TD>)>> 08:30-09:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>> 08:30-08:55<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>09:00-09:05<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>>08:55-09:00<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>09:05-09:35<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of MEG/EEG/SEEG]] - '''John Mosher, UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:35-10:00<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]] '''- Sylvain Baillet, McGill, Canada<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>10:00-10:15<<HTML(</TD><TD>)>> |
<<HTML(<TR><TD>)>>09:00-09:30<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Lecture-Slides-John.pdf|BioPhysics of MEG/EEG/SEEG]] - '''John Mosher, UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:30-9:50<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Intro-Slides-Tak.pdf|Brainstorm Overview]] - '''Takfarinas Medani, USC, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>9:50-10:00<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>10:15-10:45<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani |
<<HTML(<TR><TD>)>>10:00-10:30<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 1/5 - '''Y.Vakilna, C.Chinara, & T.Medani |
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| Review MRI volumes, surfaces, Anatomical parcellations Review raw data, event markers, EEG/MEG sensors <<HTML(<TR><TD>)>>10:45-12:15<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 2/3 - '''Y.Vakilna, C.Chinara, & T.Medani |
Review MRI volumes, surfaces <<HTML(<TR><TD>)>>10:30-12:15<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 2/5 - '''Y.Vakilna, C.Chinara, & T.Medani |
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| Review RAW recordings & events | Review recordings & events |
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| <<HTML(<TR><TD>)>>13:00-15:00<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 3/3 - '''Y.Vakilna, C.Chinara, & T.Medani | <<HTML(<TR><TD>)>>13:00-13:30<<HTML(</TD><TD>)>> '''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Slides-Christophe.pdf|BEst and NIRSTORM plugins]] - '''Christophe Grova, Concordia University, Canada<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>13:30-14:00<<HTML(</TD><TD>)>> '''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 (Demo) Automatic anatomical labeling of SEEG contacts Reviewing continuous SEEG recordings Montages and management of event markers <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>14:00-15:30<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 4/5 - '''Y.Vakilna, C.Chinara, & T.Medani |
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| Reviewing continuous SEEG recordings Montages and management of event markers Marking SEEG contacts on post-implantation image <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>15:00-15:15<<HTML(</TD><TD>)>> |
==>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 <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>15:30-15:45<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>15:15-17:00<<HTML(</TD><TD>)>> '''Advanced topics - SEEG Analsysis''' Time-frequency analysis: Identification of ictal HFO frequency bands Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways |
<<HTML(<TR><TD>)>>15:45-17:00<<HTML(</TD><TD>)>> '''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 <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>17:00<<HTML(</TD><TD>)>> '''End of the workshop''' |
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| We will 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]]. | We will provide [[https://neuroimage.usc.edu/resources/bst_workshop/2024_lax/Walkthrough-Workshop-LosAngeles-2024.docx.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)'''. |
Los Angeles, CA, USA: December 5th, 2024
Register Now: seats are very limited!
This full-day workshop will take place at the University of Southern California on Dec 5th, immediately prior to the American Epilepsy Society 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).
General information
| Where | University of Southern California (Room EEB-132) |
| When | Thursday December 5th, 2024, 8:30-17:30 |
| Instructors | Takfarinas Medani, Yash Vakilna, Chinmay Chinara, Woojae Jeong |
| Registration | Registration is now closed. |
| 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.
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:
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 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 here.
Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop.
- Download the tutorial dataset (1.5 GB):
Unzip the downloaded file on your desktop: it will create a new folder named workshopLaxMorning
- 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.
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:
- 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 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.
Download the raw data (500 MB):
Unzip the downloaded raw data on your desktop: it will create a new folder named workshopLaxAfternoon_raw
Download the pre-processed data (3 GB). 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)
workshopLaxAfternoon_raw.zip: Raw data, for SEEG localization demonstration
workshopLaxAfternoon_precomputed.zip: Pre-processed Brainstorm protocol for workshop session
Program
Thursday, December 5, 2024
| 08:30-08:55 | Registration & Check in |
| 08:55-09:00 | Introduction to the Workshop - Richard Leahy, USC, USA |
| 09:00-09:30 | BioPhysics of MEG/EEG/SEEG - John Mosher, UTH, USA |
| 09:30-9:50 | Brainstorm Overview - Takfarinas Medani, USC, USA |
| 9:50-10:00 | Coffee Break |
| 10:00-10:30 | 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 |
| 10:30-12:15 | Tutorial – Hands-On Brainstorm 2/5 - Y.Vakilna, C.Chinara, & T.Medani EEG and MEG Analysis Review 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) |
| 13:00-13:30 | BEst and NIRSTORM plugins - Christophe Grova, Concordia University, Canada |
| 13:30-14:00 | 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 (Demo) 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 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 )