BrainVISA/ Anatomist download and installation

Binary packages

Binary packages of all needed software are available on this page

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.
• Windows 98/95: There seems to be 2 main problems.
  • the package uses some environment variables, and on DOS-based versions of Windows, all variables must fit in a very limited space, so overflows are likely to happen. To overcome the problem, use a short name for the package installation directory (C:\SHFJ for instance), and remove all unnecessary environment variables before installing the package and executing programs in it. It should be enough to run BrainVisa and commandlines.
  • Anatomist starts, but often hangs (especially when controlled by BrainVisa), and the middle button (rotation) did not work for me.
  Maybe a Qt compiled on Windows XP doesnt't run well on 9x, or maybe there are network sockets incompatibilities, or maybe something else. Anyway I don't want to spend time on it, don't ask us to make it work on Windows 9x.

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 do not provide sources for the algorihm parts. We plan to open the sources of some of the algorithms but maybe not all of them, and we haven't split the libraries into "public" and "private" parts yet. As some Anatomist modules do use the algo parts, they will not be compiled and skipped by the build system.

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.

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.

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