Table of Contents
The purpose of this handbook is to provide the basic knowledge needed to start using BrainVISA.
Practical aspects such as installation and hardware recommendations will be discussed, as well as the setup of BrainVISA.
BrainVISA results from collaborative work of methodologists in neuroimaging. The goal was to provide to potential users of the methodological results a unifying environment. This environment has been designed to address the following issues:
Facilitate development, sharing and diffusion of heterogeneous neuroimaging software. The system takes into account that each software is developped independently and, therefore, can be implemented with its own programming language and can use its own data types and formats.
Provide a system to organize, share and fusion multimodal data (e.g. aMRI, fMRI, dMRI, EEG/MEG, TEP, etc.).
Allow a unified and simplified usage of neuroimaging tools through a common graphical interface.
Allow anyone to use and/or extend BrainVISA with his own tools. Therefore, BrainVISA is an open source project http://brainvisa.info.
Figure 1.1. BrainVISA management of software and data.
(a) Classical Software and data management without BrainVISA. Each user is responsible of all the interactions between programs and data. (b) BrainVISA organization. Programs and data are organized by BrainVISA and can be accessed through a unified user interface.
In the neuroscience domain, there is no standard way to organize and manage various programs and heterogenuous data. Therefore, this work is done at the user level (figure 1a). As a result, each institute, each group or even each person can have a personal unique organization stategy (when they have one). It is therefore very difficult to share data between people using different organizations. Moreover, it is often a hard work to use different programs on the same data because it is necessary to manage several incompatibilities (unit conversion, file format, 3D referential, etc...). This work has to be done for each data and it can be a fastidious repetitive task.
BrainVISA has been designed not only to provide an organization system for programs and data, but also to free users from all the technical work required to combine different programs and data. BrainVISA architecture organizes programs through a set of modules and data through a database system. A unifiying graphical interface is provided to access programs and data (figure 1b).