All the programs are in the /bin sub-folder of the package. The most frequently used programs are brainvisa, anatomist and 2 scripts for configuring your environment variables (cartopack.csh or cartopack.sh, depending on your shell).
You are not advised to add this folder to your PATH variable, as this could create conflicts with other programs in your system (for example: python, KDE, etc.). We can 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 shell. First of all, you need to identify the type of shell you are using. To do this, enter:
echo $SHELLThere are four possible results: sh, bash, csh or tcsh. According to the result:
- For sh or bash shells, enter:
. ~/my_folder/bin/cartopack.sh
- For csh or tcsh shells, enter:
source ~/my_folder/bin/cartopack.csh
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/cartopack.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 ~/.cshrc file:
alias runbv 'source ~/my_folder/bin/cartopack.csh'
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 : since the 3.0 version, 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 (but only this session).