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The practical usage of The Virtual brain in its graphical user interface and via python scripts is introduced. In the graphical user interface, you are guided through its data repository, simulator, phase plane exploration tool, connectivity editor, stimulus generator and the provided analyses. The implemented iPython notebooks of TVB are presented, and since they are public, can be used for further exploration of The Virtual brain.

Difficulty level: Beginner
Duration: 1:12:24
Speaker: : Paul Triebkorn

Get to know the TVB graphical user interface and start your first simulation. The hands-on focuses on a brief introduction to the GUI of TVB. You will visualize a structural connectome and use it for simulation. The local neural mass model will be explored through the phase plane viewer and a parameter space exploration will be performed to observe different dynamics of the large-scale brain model.

Difficulty level: Beginner
Duration: 23:21
Speaker: : Paul Triebkorn

Simulate your own stimulation with the TVB graphical user interface. This hands-on shows you how to configure a stimulus for a specific brain region and apply it to the simulation. Afterwards the results are visualized with the TVB 3D viewer.

Difficulty level: Beginner
Duration: 20:59
Speaker: : Paul Triebkorn

Explore how to setup an epileptic seizure simulation with the TVB graphical user interface. This lesson will show you how to program the epileptor model in the brain network to simulate a epileptic seizure originating in the hippocampus. It will also show how to upload and view mouse connectivity data, as well as give a short introduction to the python script interface of TVB.

Difficulty level: Intermediate
Duration: 58:06
Speaker: : Paul Triebkorn

Manipulate the default connectome provided with TVB to see how structural lesions effect brain dynamics. In this hands-on session you will insert lesions into the connectome within the TVB graphical user interface. Afterwards the modified connectome will be used for simulations and the resulting activity will be analysed using functional connectivity.

Difficulty level: Beginner
Duration: 31:22
Speaker: : Paul Triebkorn

Brain network reconstruction from empirical data is of key importance to generate personalized virtual brain models. This lecture will introduce the basic concepts of preprocessing structural, functional and diffusion weighted neuroimages. It highlights the latest methods and pipelines to extract structural as well as functional connectomes according to a multimodal parcellation.

Difficulty level: Intermediate
Duration: 1:17:32
Speaker: : Michael Schirner

Learn how to simulate strokes with the simulation platform, The Virtual Brain. We will go through two papers: Functional Mechanisms of Recovery after Stroke: Modeling with The Virtual Brain and The Virtual Brain: Modeling Biological Correlates of Recovery After Chronic Stroke, and apply the same processes with our own structural connectivity data set in The Virtual Brain.

Difficulty level: Beginner
Duration: 7:43
Speaker: : Paul Triebkorn

Learn how to simulate seizure events and epilepsy in The Virtual Brain. We will look at the paper: On the Nature of Seizure Dynamics which describes a new local model called the Epileptor, and apply this same model in The Virtual Brain. This is part 1 of 2 in a series explaining how to use the Epileptor. In this part, we focus on setting up the parameters.

Difficulty level: Beginner
Duration: 4:44
Speaker: : Paul Triebkorn

In this lecture we will focus on a paper called “The Virtual Epileptic Patient: Individualized whole-brain models of epilepsy spread”. Within their work, the authors used the epileptor model to simulate a patient's individual seizure. To understand the concept we will have a closer look at the equations of the epileptor model and particular the epileptogenicity index which controls the excitability of each brain region. Subsequently, we will begin to setup the epileptogenic zone in our own brain network model with TVB.

Difficulty level: Beginner
Duration: 6:25
Speaker: : Paul Triebkorn

After introducing the local epileptor model in the previous 2 videos we will now use it in a large scale brain simulation. We again focus on the paper “The Virtual Epileptic Patient: Individualized whole-brain models of epilepsy spread”. Two simulations with different epileptogenicity across the network are visualized to show the difference in seizure spread across the cortex.

Difficulty level: Beginner
Duration: 6:36
Speaker: : Paul Triebkorn

This lecture gives an overview on the article “Individual brain structure and modelling predict seizure propagation” where 15 subjects with epilepsy were modelled to predict individual epileptogenic zones. With the TVB GUI we will model seizure spread and the effect of lesioning the connectome. The impact of cutting edges in the network on seizure spreading will be visualized.

Difficulty level: Beginner
Duration: 9:39
Speaker: : Paul Triebkorn

This lecture briefly introduces The Virtual Brain (TVB), a multi-scale, multi-modal neuroinformatics platform for full brain network simulations using biologically realistic connectivity, as well as its potential neuroscience applications: for example with epilepsy.

Difficulty level: Beginner
Duration: 8:53
Speaker: : Petra Ritter

This lecture presents two recent clinical case studies using TVB: stroke recovery and dementia (due to Alzheimer’s Disease (AD)). Using a multi-scale neurophysiological model based on empirical multi-modal neuroimaging data, we show how local and global biophysical parameters characterize changes in  individualized patient-specific brain dynamics, predict recovery of motor function for stroke patients, and correlate with individual differences in cognition for AD patients.

Difficulty level: Intermediate
Duration: 32:11
Speaker: : Randy McIntosh
Course:

Longitudinal Online Research and Imaging System (LORIS) is a web-based data and project management software for neuroimaging research studies. It is an open source framework for storing and processing behavioural, clinical, neuroimaging and genetic data. LORIS also makes it easy to manage large datasets acquired over time in a longitudinal study, or at different locations in a large multi-site study.

Difficulty level: Beginner
Duration: 0:35
Speaker: : Samir Das

This talk highlights a set of platform technologies, software, and data collections that close and shorten the feedback cycle in research. 

Difficulty level: Beginner
Duration: 57:52
Speaker: : Satrajit Ghosh

An agent for reproducible neuroimaging

Difficulty level: Beginner
Duration: 1:00:10
Speaker: : David Kennedy

Tutorial on how to simulate brain tumor brains with TVB (reproducing publication: Marinazzo et al. 2020 Neuroimage). This tutorial comprises a didactic video, jupyter notebooks, and full data set for the construction of virtual brains from patients and health controls. Authors: Hannelore Aerts, Michael Schirner, Ben Jeurissen, DIrk Van Roost, Eric Achten, Petra Ritter, Daniele Marinazzo

Difficulty level: Intermediate
Duration: 10:01
Speaker: :

The tutorial comprises a didactic video and jupyter notebooks (reproducing publication: Falcon et al. 2016 eNeuro). Contributors: Daniele Marinazzo, Petra Ritter, Paul Triebkorn, Ana Solodkin

Difficulty level: Intermediate
Duration: 7:43
Speaker: :

This lecture was part of the 2018 Neurohackademy, a 2-week hands-on summer institute in neuroimaging and data science held at the University of Washington eScience Institute.

Difficulty level: Intermediate
Duration: 1:25:05
Speaker: : Satrajit Ghosh

This lecture introduces you to the basics of the Amazon Web Services public cloud. It covers the fundamentals of cloud computing and go through both motivation and process involved in moving your research computing to the cloud. This lecture was part of the 2018 Neurohackademy, a 2-week hands-on summer institute in neuroimaging and data science held at the University of Washington eScience Institute.

Difficulty level: Intermediate
Duration: 3:09:12
Speaker: : Amanda Tan