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
This lecture and tutorial focuses on measuring human functional brain networks. The lecture and tutorial were part of the 2019 Neurohackademy, a 2-week hands-on summer institute in neuroimaging and data science held at the University of Washington eScience Institute.
This video will teach you the basics of navigating the OSF, a free research management tool, and creating your first projects.
This webinar walks you through the basics of creating an OSF project, structuring it to fit your research needs, adding collaborators, and tying your favorite online tools into your project structure.
This webinar will introduce how to use the Open Science Framework (OSF; https://osf.io) in a Classroom. The OSF is a free, open source web application built to help researchers manage their workflows. The OSF is part collaboration tool, part version control software, and part data archive. The OSF connects to popular tools researchers already use, like Dropbox, Box, Github and Mendeley, to streamline workflows and increase efficiency.
This webinar will introduce the integration of JASP Statistical Software (https://jasp-stats.org/) with the Open Science Framework (OSF; https://osf.io). The OSF is a free, open source web application built to help researchers manage their workflows
JupyterHub is a simple, highly extensible, multi-user system for managing per-user Jupyter Notebook servers, designed for research groups or classes. This lecture covers deploying JupyterHub on a single server, as well as deploying with Docker using GitHub for authentication.
This tutorial talks about how to upload and version your data in OpenNeuro.org
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.
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.
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.
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.
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.
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.
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.