Differences between revisions 1 and 18 (spanning 17 versions)

Los Angeles, CA, USA: December 5th, 2024 [REGISTRATION NOT OPENED]

Full-day workshop, prior to the AES2024 Meeting.
This session will be an introduction to Brainstorm for iEEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops.

General information

Where	University of Southern California
When	Thursday December 5th, 2024, 8:30-17:30
Instructor	Brainstrom team
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.

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 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. 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 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.

Download the raw data:
- TBD
Unzip the downloaded raw data on your desktop: it will create a new folder named workshopUTAH_raw
Download the pre-processed data. Do not unzip this file:
- TBD
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	BioPhysics of SEEG-John Mosher, UTH, USA
11:05-11:15	Coffee Break
11:15-11:30	Brainstorm Overview-Sylvain Baillet, McGill, Canada
11:30-12:00	YYY-XXX, XXX, XXX
12:00-12:30	YYY–YYY, YYY, YYY
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 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.

Troubleshooting

For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )

-  ⇤ ← Revision 1 as of 2024-07-14 06:00:55 → 
  Size: 5035
  Editor: TakfarinasMedani
  Comment:
+   ← Revision 18 as of 2024-09-09 14:52:22 → ⇥
  Size: 6664
  Editor: TakfarinasMedani
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= Los Angeles, CA, USA: October 18th, 2023 =
<<HTML(<img align="right" alt="cutting_lax_logo.png" class="attachment" src="/brainstorm/WorkshopLA2023?action=AttachFile&amp;do=get&amp;target=cutting_lax_logo.png" title="cutting_lax_logo.png" style="width: 35%;">)>>

Half-day workshop, as part of the [[https://cuttinggardens2023.org/|CuttingGardens2023 conference]]. <<BR>> This session will be an introduction to Brainstorm for EEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops.  The link to the video will be uploaded soon.
+= Los Angeles, CA, USA: December 5th, 2024 [REGISTRATION NOT OPENED] =
Full-day workshop, prior to the [[https://aesnet.org/AES-annual-meeting|AES2024 Meeting]]. <<BR>> This session will be an introduction to Brainstorm for iEEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops.
-Line 11:
+Line 9:
-<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Wednesday October 18th, 2023: 13:00-17:30<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Thursday December 5th, 2024, 8:30-17:30<<HTML(</TD></TR>)>>
-Line 13:
+Line 11:
-<<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>[[https://neuroimage.usc.edu/brainstorm/AboutUs/RaymundoCassani|Raymundo Cassani]] & [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani#preview|Takfarinas Medani]]<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Instructor'''<<HTML(</TD><TD>)>>Brainstrom team<<HTML(</TD></TR>)>>
-Line 15:
+Line 13:
-<<HTML(<!--<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#registration|Please visit this page]]. <<HTML(</TD></TR>-->)>>
+<<HTML(<!--<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://cuttinggardens2023.org/gardens/los-angeles/#registration|T]]BD. <<HTML(</TD></TR>-->)>>
-Line 17:
+Line 15:
-<<HTML(<TR><TD>)>>'''Audience'''''' '''<<HTML(</TD><TD>)>>Users interested in analyzing EEG/MEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Audience'''''' '''<<HTML(</TD><TD>)>>Users interested in analyzing iEEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>>
-Line 28:
+Line 26:
-The workshop dataset is a pre-processed version of the dataset in 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]].
+In this workshop, we will be working on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston.
-Line 30:
+Line 28:
-Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop.
+The data is distributed as '''raw''' and '''pre-processed''' data.
-Line 32:
+Line 30:
-. Download the tutorial dataset (360 MB):
  . https://box.bic.mni.mcgill.ca/s/hKO5zc2W4uDE3Zk
 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshop_lax`'''
+. '''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
-Line 38:
+Line 51:
-  * '''`workshop_lax`''': Dataset used during the workshop session
+  * '''`workshopXXX_raw`''': Raw data, for SEEG localization demonstration
  * '''`WorkshopXXX_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session
-Line 40:
+Line 54:
-== Program ==
+== Program (TBD) ==
-Line 43:
+Line 57:
-<<HTML(<TR><TD>)>>12:30-13:00<<HTML(</TD><TD>)>>Onsite assistance in installing the material for the training session <<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>> 09:30-10:00<<HTML(</TD><TD>)>>
-Line 45:
+Line 59:
-<<HTML(<TR><TD>)>>13:00-13:30<<HTML(</TD><TD>)>>Introduction to Brainstorm (lecture)<<HTML(</TD></TR>)>>
+'''Registration, check in'''<<HTML(</TD></TR>)>>
-Line 47:
+Line 61:
-<<HTML(<TR><TD>)>>13:30-14:35<<HTML(</TD><TD>)>>'''Loading anatomy and recordings'''
+<<HTML(<TR><TD>)>>10:00-10:05<<HTML(</TD><TD>)>>
-Line 49:
+Line 63:
-Set anatomy
+'''Introduction to Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>>
-Line 51:
+Line 65:
-Review RAW recordings
+<<HTML(<TR><TD>)>>10:05-10:35<<HTML(</TD><TD>)>>
-Line 53:
+Line 67:
-Import events
+'''XXXX-'''XXXX, XXXX<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:35-11:05<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JohnMosher_slides.pdf|BioPhysics of SEEG]]-'''John Mosher, UTH, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>11:05-11:15<<HTML(</TD><TD>)>>

'''Coffee Break'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>11:15-11:30<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/SylvainBaillet_slides.pdf|Brainstorm Overview]]'''-Sylvain Baillet, McGill, Canada

<<HTML(<TR><TD>)>>11:30-12:00<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/ManishShah_slides.pdf|YYY]]'''-XXX, XXX, XXX<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>12:00-12:30<<HTML(</TD><TD>)>>

'''[[https://neuroimage.usc.edu/resources/bst_workshop/2024_parkcityutah/Slides/JayGavvala_slides.pdf|YYY]]'''–YYY, YYY, YYY<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>12:30-13:15<<HTML(</TD><TD>)>>

'''Lunch Break (Not Provided)'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>12:45-13:15<<HTML(</TD><TD>)>> Onsite assistance in installing the material for the training session<<HTML(</TD></TR>)>>
-Line 57:
+Line 97:
-<<HTML(<TR><TD>)>>14:35-15:35<<HTML(</TD><TD>)>>'''Pre-processing'''
+<<HTML(<TR><TD>)>>13:15-16:45<<HTML(</TD><TD>)>>
-Line 59:
+Line 99:
-Frequency filters
+'''Tutorial – Hands-On Brainstorm - '''Y.Vakilna, J.Hampson, T.Medani & R.Cassani
-Line 61:
+Line 101:
-Artifact detection
+<<HTML(<TR><TD>)>>13:15-14:45<<HTML(</TD><TD>)>>
-Line 63:
+Line 103:
-Artifact correction with SSP <<HTML(</TD></TR>)>>
+'''Anatomy'''
-Line 65:
+Line 105:
-<<HTML(<TR><TD>)>>15:35-15:50<<HTML(</TD><TD>)>>''Coffee break''<<HTML(</TD></TR>)>>
+Database explorer

MRI volumes, surfaces

Anatomical parcellations

Coregistration of pre- and post-implantation images
-Line 69:
+Line 115:
-<<HTML(<TR><TD>)>>15:50-16:20<<HTML(</TD><TD>)>>'''Analysis sensor level'''
+<<HTML(<TR><TD>)>>14:45-15:30<<HTML(</TD><TD>)>>
-Line 71:
+Line 117:
-Import recordings
+'''SEEG recordings'''
-Line 73:
+Line 119:
-Review trials
+Reviewing continuous SEEG recordings
-Line 75:
+Line 121:
-Trial averages
+Montages and management of event markers

Marking SEEG contacts on post-implantation image

Anatomical labeling of SEEG contacts
-Line 79:
+Line 129:
-<<HTML(<TR><TD>)>>16:20-16:55<<HTML(</TD><TD>)>>'''Source estimation'''
+<<HTML(<TR><TD>)>>15:30-15:45<<HTML(</TD><TD>)>>
-Line 81:
+Line 131:
-Forward model (aka Head model)
+'''Coffee Break'''<<HTML(</TD></TR>)>>
-Line 83:
+Line 133:
-Noise covariance matrix
+<<HTML(<TR><TD>)>>15:45-16:45<<HTML(</TD><TD>)>>
-Line 85:
+Line 135:
-Source estimation (from EEG and MEG recordings)
+'''Advanced topics - Based on participants' requests'''
-Line 87:
+Line 137:
-<<HTML(</TD></TR>)>>
+Time-frequency analysis: Identification of ictal HFO frequency bands
-Line 89:
+Line 139:
-<<HTML(<TR><TD>)>>16:55-17:15<<HTML(</TD><TD>)>>'''Analysis source level'''
+Epileptogenicity maps: Localization of the seizure onset zone and propagation pathways
-Line 91:
+Line 141:
-Cortex parcellations: Atlases and Scouts
+FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling

Open discussion with Brainstorm users

Software

Users

Development