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BrainVISA/ Anatomist download and installation


Binary packages
Binary packages of all needed software are available here :

The BrainVISA packages contain various useful software: BrainVISA Anatomist Image processing and brain segmentation software developped at the SHFJ and now at Neurospin Supporting open-source software and libraries needed by our package Supported systems (binary packages) System: Linux/i386 Version: Ubuntu 10.04 Fedora 9 Fedora 8 Fedora 7 Fedora Core 6 Fedora Core 5 Fedora Core 4 Fedora Core <= 3 Status and comments: OK OK OK OK OK

OK OK: 3.1 and 3.2 packages are built on this distribution. Not supported anymore since package 3.1 Not supported anymore since package 3.1 RedHat 9 OK for 3.0 packages which are built on this distribution. RedHat <= 8 Not supported anymore. Mandriva 2008 OK Mandriva 2007 OK Other distributions ? (not tested) OK since version 3.2. Linux/x86_64 Mandriva 2008/x86_64 (and the i386 distribution also runs on a 64-bits system). MacOS X MacOS 10.5/Intel OK, natively built on Intel since version 3.2. ? (not tested) since version 3.2. MacOS 10.4/Intel OK for version between 3.0.2 and 3.1.x, the packages are built on PPC but seem to run correctly on Intel architecture (with possibly a loss of performance). Not supported anymore since version 3.2. MacOS 10.4/PPC OK since package version 3.0.2. MacOS 10.3 Not supported anymore since package version 3.0.2. OK for 3.0.1. MacOS <= 10.2 not supported Solaris/SPARC Solaris not supported anymore Irix/MIPS4 Irix 6.5 Not supported anymore We have no Irix machine setup for compilation anymore. In

principle, building from sources should work but we cannot test it. Windows Vista XP (/NT ?) 2000 98 and earlier ? (not tested) OK globally OK (except a minor plugin that nobody will need) not supported

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.

You need about 1.5 Gb free disk space to install the BrainVISA pack 4.1. Yes, it's big, but it contains lots of useful things. Since 4.1 version, there's no setup step anymore. Each package is a file .tar.bz2 (or .zip for windows). You just have to uncompress this file and the package is ready to use. Here are the commands to uncompress the package: On Linux and MacOS:
t a rj x v f< b r a i n v i s a _ p a c k a g e > . t a r . b z 2

On Windows: unzip the zip file using whatever unzip tool you like (windows XP has one builtin in the system).

For older versions , a setup step is required. 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: cd to the directory where to install the top directory of the BrainVISA package, e.g.:
c d/ h o m e / y o u r l o g i n

uncompress the archive file:

g u n z i pc< b r a i n v i s a _ p a c k a g e > . t a r . g z|t a rx f-

On Windows, unzip the zip file using whatever unzip tool you like (windows XP has one builtin in the system). Optionally, change the main direcory name, e.g:
m v< b r a i n v i s a _ p a c k a g e >b r a i n v i s a

run the setup script:

. / b r a i n v i s a / s e t u p . s h 2/4

. / < b r a i n v i s a _ p a c k a g e > / s e t u p . s h

On Windows systems, the setup program is not a shell script (s e t u p . s h ) but an executable program: s e t u p . e x e . Just execute it like on other systems: apart from the program name extension, everything is the same. The file <brainvisa_package>.tar.gz is not longer needed (except if you want to reinstall), and can be deleted. All executable programs are in / h o m e / y o u r l o g i n / < b r a i n v i s a _ p a c k a g e > / b i n / . The most useful ones are b r a i n v i s a and a n a t o m i s t , but many many commands are provided here. A shell script can also be found in this b i ndirectory, and can be used to setup your environment variables: b v _ e n v . s h . This is only useful to debug library problems because all programs use it silently without needing you to know about it.

The package consists of two main programs, anatomist and brainvisa, and a suite of utility programs. All are located in the 'bin' directory of the package. It may be dangerous in a few cases to permanently add this directory to your path, because this can create conflicts with other programs on your system (e.g. python). We suggest two possibilities. To start a program, type the full path along with the name of the program, e.g.:
~ / < b r a i n v i s a _ p a c k a g e > / b i n / a n a t o m i s t

(or create symbolic links to 'anatomist' and 'brainvisa' in a directory listed in your path (maybe / h o m e / y o u r l o g i n / b i n ) 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 'e c h o$ S H E L L ' to determine which shell is running), you need to run: for sh or bash:
P A T H = / h o m e / y o u r l o g i n / < b r a i n v i s a _ p a c k a g e > / b i n : $ P A T H e x p o r tP A T H

for csh or tcsh:

s e t e n vP A T H/ h o m e / y o u r l o g i n / < b r a i n v i s a _ p a c k a g e > / b i n : $ P A T H

If you really wish to add it permanently in your personal config file, you may have better keep the standard / u s r / b i ndirectory first, and before the path to the binary package, for more safety. If you don't have several BrainVISA packs installed, you may just append it at the end of the P A T Hlist rather than at the beginning: sh/bash example:
P A T H = $ P A T H : / h o m e / y o u r l o g i n / < b r a i n v i s a _ p a c k a g e > / b i n e x p o r tP A T H

You can more safely add these lines in you ~ / . p r o f i l eor ~ / . b a s h r cconfig file csh/tcsh example:
s e t e n vP A T H$ { P A T H } : / h o m e / y o u r l o g i n / < b r a i n v i s a _ p a c k a g e > / b i n

Similarly, you may add this line in your ~ / . c s h r cconfig file.

Running BrainVISA
When you install BrainVISA, the data cache and generated documentations are automatically built using the following command:
b r a i n v i s au p d a t e D o c u m e n t a t i o n

You don't have to run it yourself anymore, but if you make your own processes in BrainVISA, you may have to use the u p d a t e D o c u m e n t a t i o noption. Normally, just run:
b r a i n v i s a

To delete brainvisa from your system, just remove the whole brainvisa directory (with 'r mr f< b r a i n v i s a _ p a c k a g e > ') 3/4

Optional software
Some BrainVISA processes or modules need some external software to run. See this page for details.

Other modules
BrainVISA is modular, other people may add new processes for their own tools. See the web site for more information.