Differences between revisions 9 and 17 (spanning 8 versions)

Breckenridge, Colorado, USA: March 3rd, 2025

BreckenridgeConference

Full-day of lectures and a workshop on Brainstorm as part of the International Conference on Artificial Intelligence in Epilepsy and Neurological Disorders in Breckenridge. This session will be hands-on Brainstorm features for sEEG analysis.

Participants will learn how to use Brainstorm and access its new tools on their personal laptops.

General information

Where	Breckenridge
When	March 3rd, 2025, 8:30-17:45
Registration	Please visit this page.
Organizers	AI EPILEPSY 2025
Instructors	John Mosher, Takfarinas Medani, Yash Vakilna, Johnson Hampson and Raymundo Cassani (UTH/USC USA, McGill Canada )
Audience	Users interested in analyzing sEEG/ECOG recordings using Brainstorm. Some experience with iEEG and signal processing is recommended. Teaching in English. Number of participants: XX
Slides	Intro 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 WorkshopColorado_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. Two files containing seizure onset:
  1. Seizure onset with Low-voltage-fast-activity
  2. Seizure with Ictal repetitive spiking
2. One file with interictal spike, and
3. One file containing baseline recordings
pre-processed data is located in the file workshopColorado_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:
- workshopColorado_raw.zip
Unzip the downloaded raw data on your desktop: it will create a new folder named workshopColorado_raw
Download the pre-processed data. Do not unzip this file:
- workshopColorado_precomputed.zip
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)
- workshopColorado_raw.zip: Raw data, for SEEG localization demonstration
- workshopColorado_precomputed.zip: Pre-processed Brainstorm protocol for workshop session

Program

March 3rd

08:30-08:55	Registration & Check in
08:55-09:00	Introduction to the Workshop - Richard Leahy, USC, USA
09:00-09:20	BioPhysics of SEEG - John Mosher, UTH, USA
09:20-09:40	Presentation - Speaker, institute, Country
09:40-10:00	Brainstorm Overview - Takfarinas Medani, USC, USA
10:00-10:15	Coffee Break Onsite assistance in installing the material for the training session
10:15-11:00	Tutorial – Hands-On Brainstorm 1/3 - Y.Vakilna, C.Chinara, & T.Medani (Add Johnson) Introduction to Brainstorm Interface: Anatomy Data Database explorer MRI volumes, surfaces Anatomical parcellations CT volumes Coregistration: pre- / post-implantation images
11:00-12:15	Tutorial – Hands-On Brainstorm 2/3 - Y.Vakilna, C.Chinara, & T.Medani Introduction to Brainstorm Interface: Functional Data: sEEG (We recommend you bring a mouse for this section) 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
12:15-13:00	Lunch Break (Provided? to confirm/ ask one of the sponsor sEEG??)
13:00-15:00	Tutorial – Hands-On Brainstorm 3/3 - Y.Vakilna, C.Chinara, & T.Medani SEEG Analysis ==>Import precomputed Brainstorm protocol<== sEEG Montage Configuration sEEG Frequency Analysis and Filtering Compute Forward Model (aka Head Model) Compute Noise Covariance Matrix Compute Inverse Model View Source Results Atlases and Scouts
15:00-15:15	Coffee Break (provided)
15:15-17:30	SEEG Advanced Analysis Modeling interictal spikes Modeling ictal wave within the seizure window Modeling ictal onset with LVFA at Sensor Space Modeling ictal onset with LVFA at Source Space Modeling ictal onset with repetitive spiking at Sensor and Source spaces

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).

End of the workshop, the main conference begins at 6 pm

Bring your own data

The last session will be mostly dedicated to addressing participants' requests. We encourage you to bring in your own sample of data that you would be interested in processing with Brainstorm. We may ask that you pair with other attendees, for logistics purposes.

The file formats that can be read by Brainstorm are listed on the Introduction page. Please contact us in advance if you are not sure your dataset can be imported in Brainstorm. If you do not have data available, you may continue to use the tutorial dataset used in the present workshop.

Troubleshooting

For any technical problem, please contact Takfarinas Medani ( medani@usc.edu ) & Chinmay ... Todo

-  ⇤ ← Revision 9 as of 2024-11-14 02:02:04 → 
  Size: 6455
  Editor: TakfarinasMedani
  Comment:
+   ← Revision 17 as of 2024-11-14 04:12:57 → ⇥
  Size: 8967
  Editor: ChinmayChinara
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
-Full-day of lectures and a workshop on Brainstorm as part of the International Conference on [[https://www.aiepilepsy-neuro.com/|Artificial Intelligence in Epilepsy and Neurological Disorders in Breckenridge]]. This session will be a hands-on Brainstorm features for sEEG analysis.
+Full-day of lectures and a workshop on Brainstorm as part of the International Conference on [[https://www.aiepilepsy-neuro.com/|Artificial Intelligence in Epilepsy and Neurological Disorders in Breckenridge]]. This session will be hands-on Brainstorm features for sEEG analysis.
 Line 23:
-<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> Intro slides | Walkthrough | Survey<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> Intro slides | Walkthrough | [[https://docs.google.com/forms/d/e/1FAIpQLSfLM_V2LISKa-ZPKUqrh6s4ezWFbpnUIBuLyIC1Tehw7GjZdw/viewform?usp=sf_link|Survey]]<<HTML(</TD></TR>)>>
 Line 33:
-== Workshop dataset (TBA) ==
+== Workshop dataset ==
 Line 38:
-== Program (TBA) ==
+. '''raw data''' is located in the file '''`WorkshopColorado_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 '''`workshopColorado_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://box.bic.mni.mcgill.ca/s/vJWC1ak9CW1M6YU|workshopColorado_raw.zip]]
 1. Unzip the downloaded raw data on your desktop: it will create a new folder named '''`workshopColorado_raw`'''

 1. Download the '''pre-processed data'''. Do not unzip this file:
  . [[https://box.bic.mni.mcgill.ca/s/Yqjt3sciljtHMqF|workshopColorado_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)
  * '''`workshopColorado_raw.zip`''': Raw data, for SEEG localization demonstration
  * '''`workshopColorado_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session

== Program ==
=== March 3rd ===
-Line 41:
+Line 66:
-<<HTML(<TR><TD>)>> 08:30-9:00<<HTML(</TD><TD>)>>
+<<HTML(<TR><TD>)>> 08:30-08:55 <<HTML(</TD><TD>)>>
-Line 43:
+Line 68:
-'''Registration, check in'''<<HTML(</TD></TR>)>>
+'''Registration & Check in'''<<HTML(</TD></TR>)>>
-Line 45:
+Line 70:
-<<HTML(<TR><TD>)>>09:00-09:05<<HTML(</TD><TD>)>>
+<<HTML(<TR><TD>)>>08:55-09:00<<HTML(</TD><TD>)>>
-Line 47:
+Line 72:
-'''Introduction to Workshop–'''<<HTML(</TD></TR>)>>
+'''Introduction to the Workshop - '''Richard Leahy, USC, USA<<HTML(</TD></TR>)>>
-Line 49:
+Line 74:
-<<HTML(<TR><TD>)>>09:05-12:15<<HTML(</TD><TD>)>>
+<<HTML(<TR><TD>)>>09:00-09:20<<HTML(</TD><TD>)>>
-Line 51:
+Line 76:
-'''Brainstorm Overview & Hands-On '''- '''Brainstorm team'''
+'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]] - '''John Mosher, UTH, USA<<HTML(</TD></TR>)>>
-Line 53:
+Line 78:
-<<HTML(<TR><TD>)>>12:15-13:00<<HTML(</TD><TD>)>>
+<<HTML(<TR><TD>)>>09:20-09:40<<HTML(</TD><TD>)>>
-Line 55:
+Line 80:
-'''Lunch Break '''<<HTML(</TD></TR>)>>
+'''Presentation - ''' Speaker, institute, Country<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>09:40-10:00<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]] '''- Takfarinas Medani, USC, USA<<HTML(</TD></TR>)>>
-Line 61:
+Line 90:
-<<HTML(<TR><TD>)>>10:15-10:45<<HTML(</TD><TD>)>>
+<<HTML(<TR><TD>)>>10:15-11:00<<HTML(</TD><TD>)>>
-Line 63:
+Line 92:
-'''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani
+'''Tutorial – Hands-On Brainstorm 1/3 - '''Y.Vakilna, C.Chinara, & T.Medani (Add Johnson)
-Line 65:
+Line 94:
-'''Introduction to Brainstorm Interface'''
+''' Introduction to Brainstorm Interface: Anatomy Data '''
-Line 69:
+Line 98:
-Loading anatomy and recordings
+MRI volumes, surfaces
-Line 71:
+Line 100:
-Review MRI volumes, surfaces, Anatomical parcellations
+Anatomical parcellations
-Line 73:
+Line 102:
-Review raw data, event markers, EEG/MEG sensors
+CT volumes Coregistration: pre- / post-implantation images <<HTML(</TD></TR>)>>
-Line 75:
+Line 104:
-<<HTML(<TR><TD>)>>10:45-12:15<<HTML(</TD><TD>)>>
+<<HTML(<TR><TD>)>>11:00-12:15<<HTML(</TD><TD>)>>
-Line 79:
+Line 108:
-'''EEG and MEG Analysis'''
+''' Introduction to Brainstorm Interface: Functional Data: sEEG '''
-Line 81:
+Line 110:
-Review RAW recordings & events
+'''(We recommend you bring a mouse for this section)'''
-Line 83:
+Line 112:
-Frequency filters
+Manual marking of SEEG contacts on post-implantation image
-Line 85:
+Line 114:
-Artifact detection & correction
+Automatic marking of SEEG contacts on post-implantation image
-Line 87:
+Line 116:
-'''Analysis sensor level'''
+Automatic anatomical labeling of SEEG contacts
-Line 89:
+Line 118:
-Import recordings
+Reviewing continuous SEEG recordings
-Line 91:
+Line 120:
-Review trials

Trial averages

'''Source estimation'''

Forward model (aka Head model)

Noise covariance matrix

Source estimation
+Montages and management of event markers
-Line 105:
+Line 124:
-'''Lunch Break (Provided)'''<<HTML(</TD></TR>)>>
+'''Lunch Break (Provided? to confirm/ ask one of the sponsor sEEG??)'''<<HTML(</TD></TR>)>>
-Line 111:
+Line 130:
-Reviewing continuous SEEG recordings
+==>Import precomputed Brainstorm protocol<==
-Line 113:
+Line 132:
-Montages and management of event markers
+sEEG Montage Configuration
-Line 115:
+Line 134:
-Marking SEEG contacts on post-implantation image
+sEEG Frequency Analysis and Filtering
-Line 117:
+Line 136:
-<<HTML(</TD></TR>)>>
+Compute Forward Model (aka Head Model)

Compute Noise Covariance Matrix

Compute Inverse Model

View Source Results

Atlases and Scouts
-Line 121:
+Line 148:
-'''Coffee Break'''<<HTML(</TD></TR>)>>
+'''Coffee Break (provided)'''<<HTML(</TD></TR>)>>
-Line 123:
+Line 150:
-<<HTML(<TR><TD>)>>15:15-17:00<<HTML(</TD><TD>)>>
+<<HTML(<TR><TD>)>>15:15-17:30<<HTML(</TD><TD>)>>
-Line 125:
+Line 152:
-'''Advanced topics - SEEG Analsysis'''
+'''SEEG Advanced Analysis'''
-Line 127:
+Line 154:
-Time-frequency analysis: Identification of ictal HFO frequency bands
+Modeling interictal spikes
-Line 129:
+Line 156:
-Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways
+Modeling ictal wave within the seizure window

Modeling ictal onset with LVFA at Sensor Space

Modeling ictal onset with LVFA at Source Space

Modeling ictal onset with repetitive spiking at Sensor and Source spaces
-Line 135:
+Line 168:
-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)'''.
+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)'''.
-Line 137:
+Line 170:
-End of the workshop, main conference begins at 6pm
+End of the workshop, the main conference begins at 6 pm
-Line 148:
+Line 181:
-Line 150:
+Line 182:
-For any technical problem, please contact Takfarinas Medani ( medani@usc.edu )
+For any technical problem, please contact Takfarinas Medani ( medani@usc.edu ) & Chinmay ... Todo

Software

Users

Development