|
Size: 7097
Comment:
|
← Revision 94 as of 2024-12-09 17:06:33 ⇥
Size: 9994
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Los Angeles, CA, USA: December 5th, 2024, === REGISTRATION IS NOW OPEN - Limited Places === = The full-day workshop will take place at [[https://cuttinggardens2023.org/gardens/los-angeles/#venue|University of Southern California]], on Dec 5th, a day prior to the [[https://aesnet.org/AES-annual-meeting|AES2024 Meeting]]. <<BR>> This session will introduce Brainstorm for multimodal data analysis (EEG/MEG) in the morning, and a focus on the iEEG analysis in the afternoon. Participants will learn how to use Brainstorm and access its new tools on their personal laptops. Registration is now open, please visit this [[https://my.cheddarup.com/c/brainstormworkshopla2024/items?cart|page]] to register, there is a limited number of places. |
= Los Angeles, CA, USA: December 5th, 2024 = = Register Now: seats are very limited! = <<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). Participants are invited to their personal laptops for a unique hands-on experience (data will be provided). |
| Line 11: | Line 12: |
| <<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>)>> |
| Line 15: | Line 16: |
| <<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>)>> |
| Line 21: | Line 22: |
| <<HTML(<TR><TD>)>>'''Documents'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/XRahw8lOSpgFetj|Introduction slides]] | [[https://box.bic.mni.mcgill.ca/s/rpkrUdfXUSxjArh|Walkthrough]] | [[https://forms.gle/R4g5w1A3aUNz8jMB9|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>)>> |
| Line 26: | Line 27: |
| {{{#!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. }}} |
|
| Line 30: | Line 34: |
| In this workshop, we will be working on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston. | 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. |
| Line 34: | Line 54: |
| 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: |
| Line 41: | Line 61: |
| 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. |
| Line 45: | Line 65: |
| 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]] |
| Line 55: | Line 75: |
| * '''`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 === |
| Line 61: | Line 82: |
| <<HTML(<TR><TD>)>> 08:30-09:00<<HTML(</TD><TD>)>> | <<HTML(<TR><TD>)>> 08:30-08:55<<HTML(</TD><TD>)>> |
| Line 65: | Line 86: |
| <<HTML(<TR><TD>)>>09:00-09:05<<HTML(</TD><TD>)>> '''Introduction to the Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> <<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>)>>08:55-09:00<<HTML(</TD><TD>)>> '''Introduction to the Workshop - '''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> <<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>)>> |
| Line 81: | Line 102: |
| <<HTML(<TR><TD>)>>10:15-10:45<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani '''Anatomy''' |
<<HTML(<TR><TD>)>>10:00-10:30<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 1/5 - '''Y.Vakilna, C.Chinara, & T.Medani '''Introduction to Brainstorm Interface''' |
| Line 89: | Line 110: |
| MRI volumes, surfaces Anatomical parcellations Coregistration of pre- and post-implantation images <<HTML(<TR><TD>)>>10:45-12:00<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 2/3 - '''Y.Vakilna, C.Chinara, & T.Medani '''Loading anatomy and recordings''' Set anatomy Review RAW recordings Import events '''Pre-processing''' |
Loading anatomy and recordings 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 '''EEG and MEG Analysis''' Review recordings & events |
| Line 109: | Line 124: |
| Artifact detection Artifact correction with SSP |
Artifact detection & correction |
| Line 123: | Line 136: |
| Line 131: | Line 142: |
| '''Analysis source level''' Cortex parcellation: Atlas and Scouts <<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>> |
<<HTML(<TR><TD>)>>12:15-13:00<<HTML(</TD><TD>)>> |
| Line 139: | Line 146: |
| <<HTML(<TR><TD>)>>13:00-15:00<<HTML(</TD><TD>)>> '''Tutorial – Hands-On Brainstorm 3/3 - '''Y.Vakilna, C.Chinara, & T.Medani '''SEEG recordings''' |
<<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 |
| Line 147: | Line 168: |
| Marking SEEG contacts on post-implantation image <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>15:00-15:15<<HTML(</TD><TD>)>> |
<<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 '''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 <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>15:30-15:45<<HTML(</TD><TD>)>> |
| Line 155: | Line 196: |
| <<HTML(<TR><TD>)>>15:15-17:00<<HTML(</TD><TD>)>> '''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 team/users |
<<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''' |
| Line 171: | Line 212: |
| 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]]. | 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)'''. |
| Line 174: | Line 215: |
| For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca ) | For any technical problem, please contact Takfarinas Medani ( medani@usc.edu ) |
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 )