Each download contains two files:
The binary package, for example: brainvisa-Mandriva-2008.0-x86_64-version-date.tar.bz2
The installation instructions file .README (which is also provided by the .gz file), for example brainvisa-Mandriva-2008.0-x86_64-version-date.README
Installation instructions:
Go to the folder in which you wish to install the application, for example your personal folder (which we will call /home/my_user, my_user being your first name, surname or whatever else you choose, according to the configuration of your site). Download the above-mentioned files:
cd /home/my_user
Uncompress the archive file:
tar xfj brainvisa-Mandriva-2008.0-x86_64-version-date.tar.bz2
You can rename the uncompressed folder however you wish. For example, we will call it brainvisa:
mv brainvisa-Mandriva-2008.0-x86_64-version-date brainvisa
The installation process is complete. You may delete the brainvisa-Mandriva-2008.0-x86_64-version-date.tar.bz2 file, unless you are planning another installation:
rm brainvisa-Mandriva-2008.0-x86_64-version-date.tar.bz2
All the programs are in the /bin sub-folder of the package. The most frequently used programs are brainvisa, anatomist and a script for configuring your environment variables (bv_env.sh, for sh-based shells).
You may add this folder to your PATH variable in your personal configuration files (typycally ~/.bashrc or ~/.bash_profile. We can also suggest three possible ways of initiating these programs (remember that ~ means that you are at the root of your home directory and that folder_name is the name of the folder containing the uncompressed package, for example brainvisa):
Possibility 1: To launch a program, for example anatomist, enter the absolute pathname for the program:
~/folder_name/bin/anatomist
Possibility 2: You can create symbolic links from the root of your directory to start up these programs. The commands are as follows:
cd ~
ln -s ~/folder_name/bin/anatomist anatomist
Possibility 3: You can also create a script that modifies the environment variables before each working session. These variables will only be valid for one sh-based shell.
. ~/my_folder/bin/bv_env.sh
There are two ways to avoid having to enter one of these lines every time you start your system up:
SOLUTION 1: Users of bash shells can add the following lines to their configuration file (~/.bashrc). The dot in front of the file name means that it is a hidden file. If you use an explorer to view your files, activate the Display hidden files option. Enter the following code into your ~/.bashrc file:
function brainvisa_setup
{. ~/my_folder/bin/bv_env.sh
}
As a result, when you enter brainvisa_setup you initialize your variables for a shell session (i.e. you have to run this script each time you start a new shell session). Hence, you can use the various commands from wherever you wish (brainvisa, anatomist, AimsFileInfo, etc.).
SOLUTION 2: You can also create an alias. For example, if you use a tcsh shell, define the following alias in the ~/.bashrc file:
alias runbv '. ~/my_folder/bin/bv_env.sh'
Hence, when you enter this alias, you initialize your variables, and you will be able to use the various commands from wherever you wish (brainvisa, anatomist, AimsFileInfo, etc.), for one shell session.
NOTE : environment variables are initialized from each program. If you launch this line:
~/my_folder/bin/AimfileInfoall variables will be initialised and you can use them from any directory.
Several programs are in fact available: two software packages (BrainVISA and Anatomist), along with command lines from the Aims and Vip libraries. All the programs are independent of each other.
The launching of each program depends on the configuration defined in the previous section (cf. program start-up).
To use BrainVISA (after running a script for example, cf. previous paragraph), use the following command: brainvisa.
Go to the appendix to see the options for the brainvisa command, or enter one of the following command lines:
brainvisa -hor
brainvisa --help
The Anatomist application is therefore independent of BrainVISA. You can run Anatomist alone, without running BrainVISA. Anatomist will be described in another handbook.
The launch command depends entirely on your configuration (cf. program start-up) as defined in the previous section (i.e. brainvisa_setup then anatomist).
You can also launch command lines, such as AimsFileInfo, independently of BrainVISA. Initiate a session with brainvisa_setup for example and run any command. To view information on a command, enter:
command_name -hYou will find all the commands in the /bin sub-directory or on the Web page http://brainvisa.info/doc/index_commands.html.
The launch command will depend entirely on your configuration (cf. program start-up). If you launch the script or an alias (valid for one session), you can call these commands up directly.