BrainVISA HandBook
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BrainVISA HandBook
Table of Contents
1. Introduction to BrainVISA
What is BrainVISA
Who developped BrainVISA
What is provided with BrainVISA package
Quick start
2. Installation
Checking workstation
The operating system
Recommended hardware
Downloads
Installation under Windows XP
Instructions
Using programs
Installation under Linux/Solaris/Irix
Instructions
Environment variables
Using programs
Installation under MacOS 10.5 or higher
Instructions
Uninstalling programs
3. BrainVISA User interface
General user interface
BrainVISA menu
Toolboxes panel
Processes panel
Documentation panel
BrainVISA user interface icons
Preferences window
Configuring the main options
Databases
Anatomist configuration panel
R panel
Matlab panel
SPM panel
FSL panel
Freesurfer panel
Sulci toolbox panel
User configuration
BrainVISA
log
window
Example of
log
window
Saving the
log
file
Errors window
Viewing errors
What to do in the event of an error
User interface of a process
Presentation
Menu of a parameter
Example of a process interface
Running and interrupting a process
Save the state of a process
User interface of a pipeline
User interface of an iteration
Parameter values
Example: converting several files
4. Databases and ontology
Why using BrainVISA database ?
What is a BrainVISA database ?
BrainVISA database directory organization
Example: Database organization for T1-weighted data
Database creation
Data importation
Example: Importation of a T1 MRI
Example 2: Iteration of Import T1 MRI
Importation of Dicom images
Database browser
Data history
Database update
5. Communication between BrainVISA and Anatomist
Introduction
Managing many windows
Reusable Anatomist windows
Reusable Anatomist windows blocks
Knowledge about referentials
Referentials managed by BrainVISA
Handling referentials with Anatomist
6. Parallel computing with Soma-workflow
Distributing an iteration on a multi-core machine
Bibliography
Glossary
A. Web resources
B. Options for brainvisa command line
List of Figures
1.1.
BrainVISA management of software and data.
3.1.
General user interface of BrainVISA
3.2.
Example of bug report
3.3.
Custom toolbox "Bookmarks"
3.4.
Process documentation edition window
3.5.
Preferences window
3.6.
Databases
configuration panel
3.7.
Adding a database
3.8.
Creating a database
3.9.
List of database
3.10.
Example of a Linux configuration : here we have changed the
temporaryDirectory
and Matlab
executable
fields.
3.11.
Log
interface.
3.12.
Viewing the execution of a process via the
log
interface.
3.13.
Error screen
3.14.
Error screen after a click on More info
3.15.
Process interface:
prepare subject for anatomical pipeline
3.16.
Icon animated during a process run.
3.17.
Example: the T1 segmentation pipeline.
3.18.
Window 1: Process to be iterated
3.19.
Window 2: Iteration dialog
3.20.
Window 3: Selecting files to iterate
3.21.
Window 4: Iteration window
3.22.
Window 5: Iteration completed
3.23.
Window 3.1 : After selection of
read
parameters
3.24.
Window 3.2 : Selection of
preferredFormat
parameters
3.25.
Window 3.3 : Selection of
preferredFormat
parameter
3.26.
Window 3.4 : Selection of
preferredFormat
parameter
3.27.
Window 3.5 : Validation of the first
preferredFormat
parameter
3.28.
Window 3.6 :
preferredFormat
parameters selection
4.1.
Correspondence between database directory and BrainVISA relational database
4.2.
Example of a BrainVISA database containing T1-weighted data
4.3.
Selection of Dicom files
5.1.
Reusable Anatomist windows
5.2.
Reusable Anatomist windows blocks
List of Tables
3.1.
Description of BrainVISA user interface icons
3.2.
Description of BrainVISA log user interface
3.3.
Description of process window icons: