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| <<HTML(<img align="right" alt="archildrens.png" class="attachment" src="/brainstorm/WorkshopArkansas2024?action=AttachFile&do=get&target=archildrens.png" title="archildrens_logo.png" style="width: 45%;">)>> | <<HTML(<img align="right" alt="ParkCityConference" class="attachment" src="/brainstorm/WorkshopParkCity2024?action=AttachFile&do=get&target=park_city_logo.png" title="park_city_logo.png" style="width: 50%;">)>> |
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| Half-day workshop as part of the International Conference on Artificial Intelligence in Epilepsy and Neurological Disorders in Park City https://www.aiepilepsy-neuro.com/. This session will be an introduction to Brainstorm features for sEEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops. |
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 Park City]]. This session will be an introduction to Brainstorm features for sEEG analysis. Participants will learn how to use Brainstorm and access its new tools on their personal laptops. |
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| <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://www.archildrens.org|Arkansas Children's Hospital]]<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>> [[https://www.aiepilepsy-neuro.com/content.aspx?e=1658&c=17242&culture=en-US|Park City]]<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>January 24-26, 2023, 9:00-17:00<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>April 1st, 2024, 8:30-17:00<<HTML(</TD></TR>)>> |
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| <<HTML(<!--<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://redcapwap.archildrens.org/redcap/surveys/?s=WRT4WCC4PH4P9RF3|Please visit this page]]. <<HTML(</TD></TR>-->)>> | <<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>> [[https://www.aiepilepsy-neuro.com/register.aspx?e=1658&culture=en-US|Please visit this page]]. <<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>[[https://www.archildrens.org/research/researchers/diana-escalona-vargas|Diana Escalona-Vargas]]<<BR>> (Arkansas Children's Hospital, USA)<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>''' '''[[https://www.aiepilepsy-neuro.com/|AI EPILEPSY 2024]] <<BR>> <<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Instructors'''<<HTML(</TD><TD>)>>[[AboutUs/SylvainBaillet|Sylvain Baillet]] and [[AboutUs/RaymundoCassani|Raymundo Cassani]] <<BR>> (Montreal Neurological Institute / McGill, Canada)<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Instructors'''<<HTML(</TD><TD>)>> [[https://neuroimage.usc.edu/brainstorm/AboutUs/JohnMosher|John Mosher]], [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani|Takfarinas Medani]], [[https://www.linkedin.com/in/yash-vakilna/|Yash Vakilna]], [[https://www.linkedin.com/in/johnson-hampson/|Johnson Hampson]] and [[https://neuroimage.usc.edu/brainstorm/AboutUs/RaymundoCassani|Raymundo Cassani]] <<BR>> (UTH/USC USA, McGill Canada )<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing MEG/EEG recordings using Brainstorm.<<BR>>Some experience with MEG/EEG is recommended. Teaching in English.<<BR>>Number of participants: XX <<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing sEEG/ECOG recordings using Brainstorm.<<BR>>Some experience with iEEG and signal processing is recommended. Teaching in English.<<BR>>Number of participants: XX <<HTML(</TD></TR>)>> |
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| <<HTML(<!--<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Lectures slides]] | [[https://box.bic.mni.mcgill.ca/s/XXXXXXXX|Walkthrough]] | [[https://forms.gle/XXXXXXXX|Survey]]<<HTML(</TD></TR>-->)>> | <<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>> [[https://box.bic.mni.mcgill.ca/s/sYO3hxtnd71ovFS|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/EVkBFIN9ArgcY31|Walkthrough]] | [[https://forms.gle/vGRTLzVd5C7UfFX18|Survey]]<<HTML(</TD></TR>)>> |
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| {{{#!wiki comment | |
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| TBD | In this workshop, we will be working on a SEEG dataset recorded at the Epilepsy Monitoring Unit at UTHealth Houston. |
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| 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. |
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| 1. Download the tutorial dataset (360 MB): . https://box.bic.mni.mcgill.ca/s/XXXXX 1. Unzip the downloaded file on your desktop: it will create a new folder named '''`workshop_XXXX`''' |
1. '''raw data''' is located in the file '''`WorkshopUTAH_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 '''`WorkshopUTAH_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 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: . https://box.bic.mni.mcgill.ca/s/Yqjt3sciljtHMqF |
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| * '''`workshop_XXXX`''': Dataset used during the workshop session }}} |
* '''`workshopUTAH_raw`''': Raw data, for SEEG localization demonstration * '''`WorkshopUTAH_precomputed.zip`''': Pre-processed Brainstorm protocol for workshop session |
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| === Day 1 === | === April 1st === |
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| <<HTML(<TR><TD>)>>08:30-09:00<<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>)>> |
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| <<HTML(<TR><TD>)>>09:00-10:00<<HTML(</TD><TD>)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<<HTML(</TD></TR>)>> | '''Registration, check in'''<<HTML(</TD></TR>)>> |
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| <<HTML(<TR><TD>)>>10:00-11:00<<HTML(</TD><TD>)>>'''Loading anatomy and recordings''' | <<HTML(<TR><TD>)>>10:00-10:05<<HTML(</TD><TD>)>> |
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| Brainstorm database | '''Introduction to Workshop–'''Richard Leahy, USC, USA<<HTML(</TD></TR>)>> |
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| Set anatomy | <<HTML(<TR><TD>)>>10:05-10:35<<HTML(</TD><TD>)>> |
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| Review RAW recordings | '''SEEG and the Human Brain Project-'''Philippe Ryvlin, CHUV, Switzerland<<HTML(</TD></TR>)>> |
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| Events | <<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>)>> '''Source Localization on Brainstorm'''-Manish Shah, UTH, USA<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:00-12:30<<HTML(</TD><TD>)>> '''SEEG and Multimodality Clinical Applications in Brainstorm'''–Jay Gavalla, 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>)>> |
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| <<HTML(<TR><TD>)>>11:00-12:00<<HTML(</TD><TD>)>>'''Pre-processing''' | <<HTML(<TR><TD>)>>13:15-16:45<<HTML(</TD><TD>)>> |
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| Frequency filters | '''Tutorial – Hands-On Brainstorm - '''Y.Vakilna, J.Hampson, T.Medani & R.Cassani |
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| Artifact detection | <<HTML(<TR><TD>)>>13:15-14:45<<HTML(</TD><TD>)>> |
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| Artifact correction with SSP | '''Anatomy''' Database explorer MRI volumes, surfaces Anatomical parcellations Coregistration of pre- and post-implantation images |
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| <<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>14:45-15:30<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>13:00-14:30<<HTML(</TD><TD>)>>'''Events and epoching''' | '''SEEG recordings''' |
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| Events functions | Reviewing continuous SEEG recordings |
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| Import epochs and sensor averages | Montages and management of event markers Marking SEEG contacts on post-implantation image Anatomical labeling of SEEG contacts |
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| <<HTML(<TR><TD>)>>14:30-15:00<<HTML(</TD><TD>)>> '''Spectral and time-frequency analysis of MEG/EEG signals''' ''(lecture S. Baillet)''<<HTML(</TD></TR>)>> | <<HTML(<TR><TD>)>>15:30-15:45<<HTML(</TD><TD>)>> |
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| <<HTML(<TR><TD>)>>15:00-16:30<<HTML(</TD><TD>)>>'''Time-frequency analysis''' | '''Coffee Break'''<<HTML(</TD></TR>)>> |
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| Time-frequency representation of EEG/MEG signals | <<HTML(<TR><TD>)>>15:45-16:45<<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 users |
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| === Day 2 === <<HTML(<TABLE>)>> <<HTML(<TR><TD>)>>08:30-09:00<<HTML(</TD><TD>)>>'''Source modelling''' ''(Lecture S. Baillet)''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:00-10:45<<HTML(</TD><TD>)>>'''Sources estimation''' Forward model (aka Head model) Noise covariance matrix Source estimation (surfaces and volume source spaces) Cortex parcellations: Atlases and Scouts <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>10:45-12:00<<HTML(</TD><TD>)>>'''Subject level statistics''' Statistics, sensor space Statistics, source space <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>'''ACRI Visiting Scholars Research Seminar''' ''(Lecture S. Baillet)'' <<BR>> Lunch will be provided <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>13:00-14:30<<HTML(</TD><TD>)>>'''Subject level analysis''' Subject averages (sensors, time-frequency and sources) Within subject differences <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>14:30-16:00<<HTML(</TD><TD>)>>'''Group level analysis''' Preparing sensor, time-frequency and sources data <<HTML(</TD></TR>)>> <<HTML(</TABLE>)>> === Day 3 === <<HTML(<TABLE>)>> <<HTML(<TR><TD>)>>09:00-09:30<<HTML(</TD><TD>)>>'''Connectivity & resting-state & evoked response''' ''(Lecture S. Baillet)''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>09:30-10:00<<HTML(</TD><TD>)>>'''Connectivity''' Functional connectivity <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>10:00-11:00<<HTML(</TD><TD>)>>'''Beyond the GUI''' Scripting GitHub <<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>11:00-12:00<<HTML(</TD><TD>)>>'''Participants working with their own data'''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:00-13:00<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>12:00-15:30<<HTML(</TD><TD>)>>'''Participants working with their own data'''<<HTML(</TD></TR>)>> <<HTML(<TR><TD>)>>15:30-16:00<<HTML(</TD><TD>)>>'''Wrap-up''' <<HTML(</TABLE>)>> |
End of the workshop, main conference begins at 6pm |
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| The last session will be mostly dedicated to addressing participants' requests. We encourage you to bring in your own sample of MEG/EEG data that you would be interested in processing with Brainstorm. We may ask that you pair with other attendees, for logistics purposes. | 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. |
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| For any technical problem, please contact Takfarinas Medani( [[mailto:raymundo.cassani@mcgill.ca|medani@usc.edu]] ) or Raymundo Cassani ( raymundo.cassani@mcgill.ca ) |
Park City, Utah, USA: April 1st, 2024
Full-day of lectures and a workshop on Brainstorm as part of the International Conference on Artificial Intelligence in Epilepsy and Neurological Disorders in Park City. This session will be an introduction to Brainstorm features for sEEG analysis.
Participants will learn how to use Brainstorm and access its new tools on their personal laptops.
General information
| Where | Park City |
| When | April 1st, 2024, 8:30-17:00 |
| Registration | Please visit this page. |
| Organizers | AI EPILEPSY 2024 |
| 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 WorkshopUTAH_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 WorkshopUTAH_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:
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:
- 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)
workshopUTAH_raw: Raw data, for SEEG localization demonstration
WorkshopUTAH_precomputed.zip: Pre-processed Brainstorm protocol for workshop session
Program
April 1st
| 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 Gavalla, 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 |
End of the workshop, main conference begins at 6pm
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 ) or Raymundo Cassani ( raymundo.cassani@mcgill.ca )