The Virtual Brain

Workshop: TVB:Node#5

Marseille, France

May

15

2017

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Registration & fees

Workshop has limited attendance. Break out of your resting state now!

Registration Costs:

  • Students: €100
  • Non-students: €130

Registration closes April 20th – claim your spot today!

We will serve refreshments during the coffee breaks, lunch is also provided.

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 core team, covering a broad range of topics from cutting-edge neuroscience research to advanced software development.

  • Viktor Jirsa, Marseille (France)
  • Petra Ritter, Berlin (Germany)
  • Ana Solodkin, Irvine (USA)
  • Lia Domide, Cluj-Napoca (Romania)
  • Marmaduke Woodman, Marseille (France)
  • Viktor Sip, Marseille (France)

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

    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

    Overview of the software architecture of The Virtual Brain.

  • 11:45 - 12:30

    Hands-On: Interacting with TVB using GUI

    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

    Introduction to the Python interface of The Virtual Brain.

  • 14:15 - 14:55

    From imaging data to TVB datasets: conceptual introduction

    Overview of the neuroimaging data formats, software, and steps to get TVB-compatible datasets.

  • 14:55 - 15:10

    Coffee break

  • 15:10 - 16:00

    From imaging data to TVB datasets

    Practical example of processing the neuroimaging data

  • 16:00 - 16:40

    Hands-On: Further topics in preprocessing imaging data

    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

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

  • 9:45 - 10:30

    Modeling resting state networks

    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

    Investigating the effect of strokes using TVB

    An example on how to model the structural lesions in a stroke patient.

  • 11:30 - 12:15

    Hands-On: Modeling epilepsy

    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

    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.

Location

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Aix-Marseille University

Faculty of Medicine at La Timone
27 Boulevard Jean Moulin
Pedagogical Building, Room 202
13005 Marseille, France

Organizers

This workshop is organized and hosted by the TVB team.

If you have any organizational question, please don't hesitate to send an email to our local coordinator Viktor Sip or the TVB Program Manager, Tanya Brown.

Download info

We prepared some concise PDF files to assist your visit and to help spread the word: