[PYTHON] Install The Virtual Brain

This is a memo when The virtual brain is installed on ubuntu 18.04.

Motivation

There is a simulator called The Virtual Brain that aims to create a common foundation for mathematical models of mesoscopic-level brain activity such as brain waves. It is possible to construct a mathematical model of the brain that reflects anatomical and clinical data in the structure, and generate virtual EEG and fMRI data. In short, a simulator of a coupled nonlinear oscillator system with a coupled matrix that reflects the actual structure of the brain. There are region-based model and suface-based model, and region-based model works at pc level, so I would like to install and try it.

environment

I'm not familiar with Docker, so I'll use a virtual machine this time.

official web site https://www.thevirtualbrain.org/tvb/zwei

VirtualBox_tvb1_06_11_2019_12_52_23.png

Recommended environment

https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-requirements Excerpt

download

https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-software Download the latest v1.5.8 as of November 2019. Download the Linux version 1.2GB on the right.

VirtualBox_tvb1_06_11_2019_12_56_21.png

Install and launch

$ unzip TVB_Linux_1.5.8.zip 
$ cd TVB_Distribution/

To use the web application GUI interface operated from a web browser, execute the script `tvb_start.sh``` in the `bin``` of the unzipped directory.

$ cd TVB_Distribution/bin
$ ./tvb_start.sh

When to finish

$ ./tvb_stop.sh

configuring

If you wait for a while at the first startup, the browser will open and the screen for initial settings will appear. Register the administrator user name, password, email, etc. If matlab or octave can be used, specify the path. Others are the default for the time being.

Login screen

The login screen appears. It seems that it can be accessed from the browser of other machines. So far this time.

login.png

Demo data

Some of the demo data is included in the installation package, but it seems that more data is on Github. https://github.com/the-virtual-brain/tvb-data

TODO

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