BrainVISA/ Anatomist download and installation

Binary packages

Binary packages of all needed software are available here :

The SHFJ packages contain various useful software:

• BrainVISA
• Anatomist
• Image processing and brain segmentation software developped at the SHFJ
• Supporting open-source software and libraries needed by our package

Supported systems (binary packages)

If your system is not listed in the above table and you encounter problems while installing a binary package, please upgrade your system or build from sources. We can provide binary distributions for a limited set of platforms only. Here are some known incompatibilities and possible workarounds:

• Old Linux systems: libc and some other libraries are too old and not compatible with our binary packages. Compiling might be possible with a good compiler, but nothing is guaranteed.
• OpenGL: There might be problems with some 3D graphics cards drivers under Linux or even Winwows. Read the FAQ for more details.

Source packages

Alternatively you can download the source code. These sources should compile on any UNIX platform with a decent C++ compiler, including Linux, Solaris, Irix, MacOS X. Compilation is also possible on Windows platforms in the MinGW / MSys environment. Then follow the instructions on how to compile and install the source distributions.

Note: we do not provide sources for all libraries and programs. Currently we have GPL'd the code needed to build Anatomist (data structures, IO, visualization). We provide sources for the main general algorithms, but not all algorihm parts.

Sources repository

The sources repository (subversion server) and web interface for bug tracking is accessible for open-source parts and to contributors since august 2009. This page describes how things are organized.

Installation

You need about 500 Mb free disk space to install the SHFJ pack 3.0. Yes, it's big, but it contains lots of useful things.

Each binary package is a single .tar.gz file, plus a .README file with installation instructions (it is also provided in the tar file). The instructions here are a copy of this README file:

1. cd to the directory where to install the top directory of the BrainVISA package, e.g.:
   

     cd /home/yourlogin

2. uncompress the archive file:
   

     gunzip -c SHFJ_pack-stable-linux-3.0.0.tar.gz | tar xf -

   On Windows, unzip the zip file using whatever unzip tool you like (windows XP has one builtin in the system).
3. Optionally, change the main direcory name, e.g:
   

     mv SHFJ_pack-stable-linux-3.0.0 brainvisa

4. run the setup script:
   

     ./brainvisa/setup.sh

   or:
   

     ./SHFJ_pack-stable-linux-3.0.0/setup.sh

   On Windows systems, the setup program is not a shell script (setup.sh) but an executable program: setup.exe. Just execute it like on other systems: apart from the program name extension, everything is the same.
5. The file SHFJ_pack-stable-linux-3.0.0.tar.gz is not longer needed (except if you want to reinstall), and can be deleted.

All executable programs are in /home/yourlogin/SHFJ_pack-stable-linux-3.0.0/bin/. The most useful ones are brainvisa and anatomist, but many many commands are provided here.
Two shell scripts can also be found in this bin directory, and can be used to setup your environment variables: SHFJEnvironmentVariables.csh and SHFJEnvironmentVariables.sh (depending on your shell). They are now only useful to debug library problems because all programs use them silently without needing you to know about them.

Running

1. To start a program, type the full path along with the name of the program, e.g.:

     ~/SHFJ_pack-stable-linux-3.0.0/bin/anatomist

   (or create symbolic links to 'anatomist' and 'brainvisa' in a directory listed in your path (maybe /home/yourlogin/bin)
   
2. If you often launch anatomist, brainvisa or the accompanying programs, you can run a small shell script that modifies the path before each working session. Depending on your shell (bash, csh...; use 'echo $SHELL' to determine which shell is running), you need to run:
   
   for sh or bash:

     PATH=/home/yourlogin/SHFJ_pack-stable-linux-3.0.0/bin:$PATH
     export PATH

   for csh or tcsh:

     setenv PATH /home/yourlogin/SHFJ_pack-stable-linux-3.0.0/bin:$PATH

   If you really wish to add it permanently in your personal config file, you may have better keep the standard /usr/bin directory first, and before the path to the binary package, for more safety. If you don't have several SHFJ packs installed, you may just append it at the end of the PATH list rather than at the beginning:
   sh/bash example:

     PATH=$PATH:/home/yourlogin/SHFJ_pack-stable-linux-3.0.0/bin
     export PATH

   You can more safely add these lines in you ~/.profile or ~/.bashrc config file
   csh/tcsh example:

     setenv PATH ${PATH}:/home/yourlogin/SHFJ_pack-stable-linux-3.0.0/bin

   Similarly, you may add this line in your ~/.cshrc config file.

Running BrainVISA

brainvisa --updateDocumentation

brainvisa

Uninstalling

Optional software

Other modules