The Virtual Brain

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

The workshop has been strategically scheduled to take place preceding the annual Brain Connectivity Workshop that will take place May 17-19 in Zurich, Switzerland.

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

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. Applications to use cases in the healthy and diseased brain are explicitly presented.

Workshop format: lectures and hands-on tutorials. Participants are encouraged to bring their own data to work on.

Workshop program overview:

• Theoretical background of large scale brain network modelling
  
• Architecture of The Virtual Brain (TVB)
• Interacting with TVB using GUI and Python interface
  
• Preprocessing neuroimaging data, or how to obtain a TVB dataset
• Fitting the brain model parameters to the functional data
  
• Modeling resting state network dynamics in fMRI
• Modeling stroke and recovery
  
• Modeling epilepsy and surgical interventions
  
• Modifying TVB code and implementing new features
  
• Bring your own data hands-on sessions: preprocessing and simulations

Prepare your gear

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:

• Download and install the latest stable TVB package.
• Test it in its current form to make sure it's compatible with your computing environment.
• Familiarize yourself with the basics by browsing through the included manual (TVB-Distribution/docs/UserManual.pdf).
• 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 user forum on Google Groups

Meet the TVB team

Apart from learning together, you can meet and talk to a good part of The Virtual Brain's team, covering a broad range of topics from cutting-edge neuroscience research to advanced software development.

Program: DAY 1 Morning Session

• 08:30 - 09:00

  Registration & caffeine intake

• 09:00 - 09:15

  Introduction

• 09:15 - 10:45

  A generative model of the brain: Describing the building blocks of a brain network model
  :: VIKTOR JIRSA

  Basic principles and assumptions, recent studies with different local models, approximation of neural fields.

• 10:45 - 11:00

  Coffee break

• 11:00 - 11:45

  Architecture of TVB
  :: LIA DOMIDE/PAULA POPA

  Overview of the software architecture of The Virtual Brain.

• 11:45 - 12:30

  Hands-On: Interacting with TVB using GUI
  :: LIA DOMIDE/PAULA POPA

  Learn to prepare and run TVB simulations through web interface.

• 12:30 - 13:30

  Lunch break

Program: DAY 1 Afternoon Session

• 13:30 - 14:15

  Hands-On: Interacting with TVB using CLI
  :: LIA DOMIDE/PAULA POPA

  Introduction to the Python interface of The Virtual Brain.

• 14:15 - 14:55

  Imaging data pipeline: step-by-step towards personalized brain models
  :: PETRA RITTER

  How multimodal imaging data (DTI, T1-MRI, fMRI, EEG) are processed for TVB import using an existing and tested pipeline.

• 14:55 - 15:10

  Coffee break

• 15:10 - 16:00

  Practical example how to prepare imaging data for TVB use and how to upload them to TVB
  :: PETRA RITTER

  Step-by step demos

• 16:00 - 16:40

  Hands-On: Further topics in preprocessing imaging data
  :: MARMADUKE WOODMAN

  How to obtain gain matrices for MEG, EEG and sEEG recordings.

• 16:40 - 17:20

  (Optional) Hands-On: Bring your own data: preprocessing

  Hands-on session for participants with their own data.

Program: DAY 2 Morning Session

• 08:30 - 09:00

  Morning caffeine

• 9:00 - 9:45

  Data fitting: theoretical background
  :: MEYSAM HASHEMI

  Fitting the model outputs and the measurements: parameter sweeps, Bayesian inference.

• 9:45 - 10:30

  Hands-On: Modeling resting state networks
  :: JULIE COURTIOL

  Modeling resting state networks and exploring their dynamics using the subjects from the Human Connectome Project database.

• 10:30 - 10:45

  Coffee break

• 10:45 - 11:30

  Clinical application of TVB
  :: ANA SOLODKIN

  From stroke to Alzheimer's Disease.

• 11:30 - 12:15

  Hands-On: Modeling epilepsy
  :: VIKTOR SIP

  Modeling partial seizure propagation for specific patients.

• 12:15 - 13:15

  Lunch break

Program: DAY 2 Afternoon Session

• 13:15 - 14:15

  Hands-On: Modifying TVB code and implementing new features
  :: MARMADUKE WOODMAN

  A guide on how to add a new neural mass model, integration scheme, or a monitor to the code of TVB.

• 14:15 - 14:25

  Closing remarks

• 14:25 - 14:40

  Coffee break

• 14:40 - 17:20

  (Optional) Hands-On: Bring your own data

  Setting up and running the simulations under the supervision of TVB experts.