|
Size: 5035
Comment:
|
Size: 7056
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | 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&do=get&target=cutting_lax_logo.png" title="cutting_lax_logo.png" style="width: 35%;">)>> |
= Los Angeles, CA, USA: December 5th, 2024 = ---- /!\ '''Edit conflict - other version:''' |
| Line 4: | Line 5: |
| 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. | ---- <<HTML(<img align="right" alt="cutting_lax_logo.png" class="attachment" src="/brainstorm/WorkshopLA2023?action=AttachFile&do=get&target=cutting_lax_logo.png" title="USC.jpg" style="width: 35%;">)>> Full-day workshop, prior of the [[https://aesnet.org/AES-annual-meeting|AES2023 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 15: |
| <<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>)>>Thursdya December 5th, 2024, 8:30-17:30<<HTML(</TD></TR>)>> |
| Line 13: | Line 17: |
| <<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 19: |
| <<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 21: |
| <<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 32: |
| 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 34: |
| 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 36: |
| 1. 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`''' |
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: 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 57: |
| * '''`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 60: |
| == Program == | == Program (TBD) == |
| Line 43: | Line 63: |
| <<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 65: |
| <<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 67: |
| <<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 69: |
| Set anatomy | '''Introduction to Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> |
| Line 51: | Line 71: |
| Review RAW recordings | <<HTML(<TR><TD>)>>10:05-10:35<<HTML(</TD><TD>)>> |
| Line 53: | Line 73: |
| Import events | '''SEEG and the Human Brain Project-'''Philippe Ryvlin, CHUV, Switzerland<<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|Source Localization on Brainstorm]]'''-Manish Shah, UTH, USA<<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|SEEG and Multimodality Clinical Applications in Brainstorm]]'''–Jay Gavvala, UTH, USA<<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 103: |
| <<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 105: |
| Frequency filters | '''Tutorial – Hands-On Brainstorm - '''Y.Vakilna, J.Hampson, T.Medani & R.Cassani |
| Line 61: | Line 107: |
| Artifact detection | <<HTML(<TR><TD>)>>13:15-14:45<<HTML(</TD><TD>)>> |
| Line 63: | Line 109: |
| Artifact correction with SSP <<HTML(</TD></TR>)>> | '''Anatomy''' |
| Line 65: | Line 111: |
| <<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 121: |
| <<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 123: |
| Import recordings | '''SEEG recordings''' |
| Line 73: | Line 125: |
| Review trials | Reviewing continuous SEEG recordings |
| Line 75: | Line 127: |
| Trial averages | Montages and management of event markers Marking SEEG contacts on post-implantation image Anatomical labeling of SEEG contacts |
| Line 79: | Line 135: |
| <<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 137: |
| Forward model (aka Head model) | '''Coffee Break'''<<HTML(</TD></TR>)>> |
| Line 83: | Line 139: |
| Noise covariance matrix | <<HTML(<TR><TD>)>>15:45-16:45<<HTML(</TD><TD>)>> |
| Line 85: | Line 141: |
| Source estimation (from EEG and MEG recordings) | '''Advanced topics - Based on participants' requests''' |
| Line 87: | Line 143: |
| <<HTML(</TD></TR>)>> | Time-frequency analysis: Identification of ictal HFO frequency bands |
| Line 89: | Line 145: |
| <<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 147: |
| Cortex parcellations: Atlases and Scouts | FEM demo: MRI segmentation, tissue anisotropy with DTI, FEM forward modeling Open discussion with Brainstorm users |
Los Angeles, CA, USA: December 5th, 2024
![/!\](/moin_static198/brainstorm1/img/alert.png "/!\"){kind=small}
Edit conflict - other version:
Full-day workshop, prior of the AES2023 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 | Thursdya 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:
- 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 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 | SEEG and the Human Brain Project-Philippe Ryvlin, CHUV, Switzerland |
| 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 | Source Localization on Brainstorm-Manish Shah, UTH, USA |
| 12:00-12:30 | SEEG and Multimodality Clinical Applications in Brainstorm–Jay Gavvala, UTH, USA |
| 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 )