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

Ubuntu 18.04 (desktop)

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

I want to use it as a server from another machine.
It depends on whether it will be a web interface or a script, but for the time being, I will try using it from the web.

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

Recommended environment

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

1 1 CPU core is required for simulation.
8GB or more of memory is sufficient for one region-level simulation. At least 16GB or more for more complex simulations.
Surface-level simulation requires more memory
300MB of disk space is required for surface-level 10ms simulation. A guideline is 50GB per user.
When using a PC, a WebGL compatible graphic card is required.

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.

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.

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

Is it convenient to create a dedicated user and move from there to use it in a multi-user setting?

Install The Virtual Brain