This lecture gives an overview of how to prepare and preprocess neuroimaging (EEG/MEG) data for use in TVB.  

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.

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. 

This lecture covers the needs and challenges involved in creating a FAIR ecosystem for neuroimaging research.

This lecture covers the NIDM data format within BIDS to make your datasets more searchable, and how to optimize your dataset searches.

This lecture covers the processes, benefits, and challenges involved in designing, collecting, and sharing FAIR neuroscience datasets.

This lecture covers positron emission tomography (PET) imaging and the Brain Imaging Data Structure (BIDS), and how they work together within the PET-BIDS standard to make neuroscience more open and FAIR.

This lecture covers the benefits and difficulties involved when re-using open datasets, and how metadata is important to the process.

This lecture provides guidance on the ethical considerations the clinical neuroimaging community faces when applying the FAIR principles to their research. 

This lesson provides an overview of the Miniscope project, explaining the motivation behind the how and why of Miniscope development, why Miniscopes may be useful for researchers, and the differences between previous and current versions.

This lesson provides instruction on how to build a Miniscope and stream data, including an overview of the software involved.

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.

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.

This lesson explains the fundamental principles of neuronal communication, such as neuronal spiking, membrane potentials, and cellular excitability, and how these electrophysiological features of the brain may be modelled and simulated digitally. 

This is a tutorial on how to simulate neuronal spiking in brain microcircuit models, as well as how to analyze, plot, and visualize the corresponding data. 

This is an in-depth guide on EEG signals and their interaction within brain microcircuits. Participants are also shown techniques and software for simulating, analyzing, and visualizing these signals.

In this tutorial on simulating whole-brain activity using Python, participants can follow along using corresponding code and repositories, learning the basics of neural oscillatory dynamics, evoked responses and EEG signals, ultimately leading to the design of a network model of whole-brain anatomical connectivity. 

This lecture focuses on the structured validation process within computational neuroscience, including the tools, services, and methods involved in simulation and analysis.

This session will include presentations of infrastructure that embrace the FAIR principles developed by members of the INCF Community.

This lecture provides an overview of The Virtual Brain Simulation Platform.

This lesson contains practical exercises which accompanies the first few lessons of the Neuroscience for Machine Learners (Neuro4ML) course.