BrainVISA HandBook - Version 3.1
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BrainVISA HandBook - Version 3.1
Table of Contents
1. Introduction to BrainVISA
What is BrainVISA
What is provided with BrainVISA package version 3.1
Who developped BrainVISA
2. Configuring your workstation
The operating system
Recommended hardware
3. Installation under Windows XP
Downloads
Instructions
Using programs
Program: BrainVISA
Program: Anatomist
Command lines
Uninstalling programs
4. Installation under Linux/Solaris/Irix
Downloads
Instructions
Environment variables
Using programs
Program: BrainVISA
Program: Anatomist
Command lines
Uninstalling programs
5. Installation under MacOS 10.4
Instructions
6. BrainVISA User interface
General user interface
BrainVISA menu
Process access window
Current process information window
BrainVISA user interface icons
Configuring BrainVISA
Configuring the main options
Databases
Anatomist configuration panel
R panel
Matlab panel
User configuration
Bug report: setup and use
User interface of a process
Presentation
Example of a process interface
Running and interrupting a process
Monitoring processes
Managing errors
Iterative process mode
7. Data structure
Introduction
Organization of directories
Data formats
Data Management: importing a T1 MRI
Introduction
Importing a T1 weighted image
Working without a BrainVISA database
8. Communication between BrainVISA and Anatomist
Introduction
Knowledge about referentials
Referentials managed by BrainVISA
Handling referentials with Anatomist
9. In brief
Philosophy of BrainVISA
Configuration of BrainVISA
Data organization
Bibliography
Glossary
A. Web resources
B. Options for brainvisa command line
List of Figures
1.1.
BrainVISA management of software and data.
4.1.
Installation window
6.1.
General user interface of BrainVISA
6.2.
Preferences window
6.3.
Databases
configuration panel
6.4.
Adding a database
6.5.
Creating a database
6.6.
List of database
6.7.
Example of a Linux configuration : here we have changed the
temporaryDirectory
and Matlab
executable
fields.
6.8.
Configuration of the
Support function
6.9.
Sending of bug report
6.10.
Process interface:
prepare subject for anatomical pipeline
6.11.
Icon animated during the running of a process.
6.12.
Log
file interface.
6.13.
Viewing the execution of a process via the
log
file interface.
6.14.
Error screen
6.15.
Error message: the T1mri field has not been completed
6.16.
Incompatible input data
6.17.
Window 1: Process to be iterated
6.18.
Window 2: Iterative mode
6.19.
Window 3: Selecting files to iterate
6.20.
Window 4: Processing the files to be iterated
6.21.
Window 5: Iteration completed
6.22.
Window 3.1 : After selection of
read
parameters
6.23.
Window 3.2 : Selection of
preferredFormat
parameters
6.24.
Window 3.3 : Selection of
preferredFormat
parameter
6.25.
Window 3.4 : Selection of
preferredFormat
parameter
6.26.
Window 3.5 : Validation of the first
preferredFormat
parameter
6.27.
Window 3.6 :
preferredFormat
parameters selection
7.1.
Example of a BrainVISA database
List of Tables
2.1.
List of operating systems and versions compatible with binary packages
6.1.
Description of BrainVISA user interface icons
6.2.
Description of process window icons:
6.3.
Description of BrainVISA user interface log file