Skip to main content

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

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

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

As a part of NeuroHackademy 2020, Tara Madhyastha (University of Washington), Andrew Crabb (AWS), and Ariel Rokem (University of Washington) give a lecture on Cloud Computing, focusing on Amazon Web Services

 

This video is provided by the University of Washington eScience Institute.

 

Difficulty level: Beginner
Duration: 01:43:59
Speaker: :

Shawn Brown presents an overview of CBRAIN, a web-based platform that allows neuroscientists to perform computationally intensive data analyses by connecting them to high-performance-computing facilities across Canada and around the world.

 

This talk was given in the context of a Ludmer Centre event in 2019.

 

 

Difficulty level: Beginner
Duration: 56:07
Speaker: :

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.

Difficulty level: Intermediate
Duration: 50:44
Speaker: : Caterina Gratton

Lecture on functional brain parcellations and a set of tutorials on bootstrap agregation of stable clusters (BASC) for fMRI brain parcellation which 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.

Difficulty level: Advanced
Duration: 50:28
Speaker: : Pierre Bellec

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
Course:

BioImage Suite is an integrated image analysis software suite developed at Yale University. BioImage Suite has been extensively used at different labs at Yale since about 2001.

Difficulty level: Beginner
Duration: 01:47
Speaker: : BioImage Suite
Course:

Fibr is an app for quality control of diffusion MRI images from the Healthy Brain Network, a landmark mental health study that is collecting MRI images and other assessment data from 10,000 New York City area children. The purpose of the app is to train a computer algorithm to analyze the Healthy Brain Network dataset. By playing fibr, you are helping to teach the computer which images have sufficiently good quality and which images do not. 

Difficulty level: Beginner
Duration: 02:26
Speaker: : Ariel Rokem

This module covers many of the types of non-invasive neurotech and neuroimaging devices including Electroencephalography (EEG), Electromyography (EMG), Electroneurography (ENG), Magnetoencephalography (MEG), functional Near-Infrared Spectroscopy (fNRIs), Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET), and Computed Tomography

Difficulty level: Beginner
Duration: 13:36
Speaker: : Harrison Canning
Course:

An introduction to data management, manipulation, visualization, and analysis for neuroscience. Students will learn scientific programming in Python, and use this to work with example data from areas such as cognitive-behavioral research, single-cell recording, EEG, and structural and functional MRI. Basic signal processing techniques including filtering are covered. The course includes a Jupyter Notebook and video tutorials.

 

Difficulty level: Beginner
Duration: 1:09:16
Speaker: : Aaron J. Newman
Course:

This book was written with the goal of introducing researchers and students in a variety of research fields to the intersection of data science and neuroimaging. This book reflects our own experience of doing research at the intersection of data science and neuroimaging and it is based on our experience working with students and collaborators who come from a variety of backgrounds and have a variety of reasons for wanting to use data science approaches in their work. The tools and ideas that we chose to write about are all tools and ideas that we have used in some way in our own research. Many of them are tools that we use on a daily basis in our work. This was important to us for a few reasons: the first is that we want to teach people things that we ourselves find useful. Second, it allowed us to write the book with a focus on solving specific analysis tasks. For example, in many of the chapters you will see that we walk you through ideas while implementing them in code, and with data. We believe that this is a good way to learn about data analysis, because it provides a connecting thread from scientific questions through the data and its representation to implementing specific answers to these questions. Finally, we find these ideas compelling and fruitful. That’s why we were drawn to them in the first place. We hope that our enthusiasm about the ideas and tools described in this book will be infectious enough to convince the readers of their value.

 

Difficulty level: Intermediate
Duration:
Speaker: :
Course:

This Jupyter Book is a series of interactive tutorials about quantitative T1 mapping, powered by qMRLab. Most figures are generated with Plot.ly – you can play with them by hovering your mouse over the data, zooming in (click and drag) and out (double click), moving the sliders, and changing the drop-down options. To view the code that was used to generate the figures in this blog post, hover your cursor in the top left corner of the frame that contains the tutorial and click the checkbox “All cells” in the popup that appears.

Jupyter Lab notebooks of these tutorials are also available through MyBinder, and inline code modification inside the Jupyter Book is provided by Thebelab. For both options, you can modify the code, change the figures, and regenerate the html that was used to create the tutorial below. This Jupyter Book also uses a Script of Scripts (SoS) kernel, allowing us to process the data using qMRLab in MATLAB/Octave and plot the figures with Plot.ly using Python, all within the same Jupyter Notebook.

Difficulty level: Intermediate
Duration:
Speaker: :

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 tutorial by Paul Triebkorn on how to simulate using TVB is part of the TVB Node 10 series, a 4 day workshop dedicated to learning about The Virtual Brain, brain imaging, brain simulation, personalised brain models, TVB use cases, etc. TVB is a full brain simulation platform.

Difficulty level: Intermediate
Duration: 1:29:13
Speaker: : Paul Triebkorn

 

This tutorial on simulating The Virutal Mouse Brain by Patrik Bey is part of the TVB Node 10 series, a 4 day workshop dedicated to learning about The Virtual Brain, brain imaging, brain simulation, personalised brain models, TVB use cases, etc... TVB is a full brain simulation platform.

Difficulty level: Intermediate
Duration: 42:43
Speaker: : Patrik Bey

This tutorlal on modeling a virtual macaque brain by Julie Courtiol is part of the TVB Node 10 series, a 4 day workshop dedicated to learning about The Virtual Brain, brain imaging, brain simulation, personalised brain models, TVB use cases, etc. TVB is a full brain simulation platform.

Difficulty level: Intermediate
Duration: 1:00:08
Speaker: : Julie Courtiol

This lecture on multi-scale entropy by Jil Meier is part of the TVB Node 10 series, a 4 day workshop dedicated to learning about The Virtual Brain, brain imaging, brain simulation, personalised brain models, TVB use cases, etc. TVB is a full brain simulation platform.

Difficulty level: Intermediate
Duration: 39:05
Speaker: : Jil Meier