The Virtual Brain

2 DAY WORKSHOP :: MAY 20-21, 2019

Get up to speed about the fundamental principles of full brain network modeling using the open-source neuroinformatics platform The Virtual Brain (TVB).

TVB NODE#8 has been strategically scheduled to take place ahead of NeuroFrance 2019. Be sure to register for both!

TVB enables biologically realistic modeling of network dynamics using Connectome-based approaches across different brain scales.

Generate macroscopic neuroimaging signals including fMRI, intracranial and stereotactic EEG, surface EEG and MEG for single subjects.

Personalized brain network models can be derived from an individual’s MRI data.

Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python. Applications to use cases in the healthy and diseased brain are explicitly presented.

Simulated brains. Real memories.

In the workshop we will explain the fundamental principles of full brain network modeling using the open source neuroinformatics platform The Virtual Brain (TVB). This simulation environment enables the biologically realistic modeling of network dynamics using connectome-based approaches across different brain scales. Configurable brain network models generate macroscopic neuroimaging signals including functional MRI, intracranial and stereotactic EEG, surface EEG and MEG for single subjects. Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python.

WORKSHOP FORMAT:

• Lectures and hands-on tutorials
  
• Participants are encouraged to bring their own data to work on
  

Program: DAY 1

• 08:30 - 09:00

  Arrival, registration & coffee

• 09:00 - 09:15

  Introduction to Node 8 workshop

• 09:15 - 10:45

  A generative model of the brain
  Describing the building blocks of a brain network model: basic principles and assumptions
  VIKTOR JIRSA - AIX-MARSEILLE UNIVERSITÉ, FRANCE

• 10:45 - 11:00

  Coffee Break
  

• 11:00 - 11:45

  Architecture of TVB
  Overview of the software architecture of TVB
  MIHAI ANDREAI - CODEMART, ROMANIA

• 11:45 - 12:30

  Hands-On:: Interacting with TVB using GUI
  Learn to prepare and run TVB simulations through web interface
  PAUL TRIEBKORN - CHARITÉ, GERMANY

• 12:30 - 13:30

  Lunch break
  Lunch will be provided
  

• 13:30 - 14:15

  Hands-On:: Interacting with TVB using CLI
  Learn to prepare and run TVB simulations through the Python interface
  PAUL TRIEBKORN - CHARITÉ, GERMANY

• 14:15 - 15:00

  TVB Clinical Applications - Part I: Epilepsy
  VIKTOR SIP - AIX-MARSEILLE UNIVERSITÉ, FRANCE

• 15:00 - 15:15

  Coffee Break
  

• 15:15 - 16:00

  Data fitting: theoretical background
  Fitting the model outputs and the measurements: parameter sweeps, Bayesian inference
  MEYSAM HASHEMI - AIX-MARSEILLE UNIVERSITÉ, FRANCE

• 16:00 - 16:45

  Hands-On:: Modeling epilepsy
  How to simulate a virtual epileptic patient?
  JULIE COURTIOL - CHARITÉ, GERMANY

• 16:45 - 17:30

  TVB Clinical Applications - Part II: Brain tumors
  HANNELORE AERTS - GHENT UNIVERSITY, BELGIUM

Program: DAY 2

• 09:00 - 09:15
  

  Morning caffeine

• 9:15 - 10:00

  Personalization pipeline
  PAULA POPA - CODEMART
  PAUL TRIEBKORN - CHARITÉ, GERMANY

• 10:00 - 10:45

  TVB Use-case: Resting-state
  JULIE COURTIOL - CHARITÉ, GERMANY

• 10:45 - 11:00

  Coffee Break
  

• 11:00 - 11:45

  Hands-On:: Modeling resting-state
  How to simulate the experimental rest condition?
  JULIE COURTIOL - CHARITÉ, GERMANY
  

• 11:45 - 12:30

  TVB Use-case: Brain stimulation
  SORA AN - AIX-MARSEILLE UNIVERSITÉ, FRANCE

• 12:30 - 13:30

  Lunch break
  Lunch will be provided
  

• 13:30 - 14:15

  TVMB: The Virtual Mouse Brain
  FRANCESCA MELOZZI - AIX-MARSEILLE UNIVERSITÉ, FRANCE

• 14:15 - 15:00

  Hands-On:: Modeling mouse brain activity
  How to simulate brain activity in mouse at rest?
  PAUL TRIEBKORN - CHARITÉ, GERMANY

• 15:00 - 15:15

  Coffee Break
  

• 15:15 - 16:00 *

  Hands-On:: Modifying TVB code and implementing new features
  LIONEL KUSCH - AIX-MARSEILLE UNIVERSITÉ, FRANCE

• 16:00 - 16.15

  Concluding words

PREPARE FOR THE WORKSHOP

To get the most out of this workshop as an attendee, you might want to get a head-start by preparing your gear before you arrive:

1) Download and install the latest stable TVB package.
2) Test it in its current form to make sure it's compatible with your computing environment.
3) Familiarize yourself with the basics by browsing through the included manual.(after TVB is downloaded, located at /TVB-Distribution/docs/UserManual.pdf)
4) If you are interested in modifying the code and contributing to TVB, also install the version control system Git.

In case of any technical problems with TVB installation, head over to the TVB mailing list

IMPORTANT DETAILS:

Equipment. Please bring your own laptops to work on, and follow the steps below to prepare your software environment.

Lodging. Participants are responsible for their accommodation.