BrainVISA readme / release notes
Last modification: October 9, 2009
Add-on module packages
All contributors of BrainVISA project are very happy to propose tools, libraries, demonstration data and documentation available free of charge on http://brainvisa.info. The BrainVISA project is focused on neuroimaging and the development of tools only in a context of research. Although every care has been taken by all contributors of the BrainVISA project no warranty can be given in respect of the accuracy, reliability, up-to-dateness or completeness of the information contained within BrainVISA project.
In the same way no one will be responsible or liable for any loss or damage of any sort.
Any contributor reserves the right to alter or remove the content, in full or in part, without prior notice.
All programs and software libraries present in the binary distributions do not have the same licence.
External software come with their own licence, which may depend on the
system. For instance, PyQt is under GPL on Unix, and under a commercial licence on Windows. All other included software are open-source and under GPL, LGPL or BSD-like licences.
Our open-source software is governed by CeCILL license version 2 for the parts that depend on PyQt and under CeCILL-B license for other parts, under French law and abiding by the rules of distribution of free software.
You can use, modify and/or redistribute the software under the
terms of the licences as circulated by CEA, CNRS and INRIA at the following URL http://www.cecill.info.
But we also have closed-source programs. They can be freely copied and redistributed as binaries. But they are not released under the CeCill license, and are not using CeCill nor GPL software.
Contents of the package
BrainVISA is packaged together with many software. The distribution contains all the
core open-source software of BrainVisa itself and of our image analysis libraries. It also includes all our algorithms which are closed-source but binaries are provided
for free. Additionally, several third-party software programs and libraries are packed
in the bundle (especially the Python language interpreter and many modules).
- Aims : Freeware libraries from our lab, with their sets of commandlines
- Some closed-source libraries and programs from our lab
- Freeware libraries: libsigc++, libxml2, DcmTk, Ecat library, Minc and netcdf libraries
- Qt, used for all GUI
- Qwt: additional widgets for Qt (mainly for curves plotting)
- The Python interpreter
- Various modules for python, including:
- XML modules
- numpy: array and matrix manipulation library
- PyQt: python bindings for Qt
- PyQwt: python bindings for Qwt
- IPython: an enhanced python shell
- SciPy is present on some distributions, but not on all systems
- pymat, a matlab module for python. This module is compiled for matlab 6.x in the
binary distribution. If you need a module for another version (matlab 7), it needs to
be recompiled using the matching libraries from matlab (matlab engine library).
- On Unix/X11 distributions, a gnuplot module is also present
- pySqlite : python bindings for the database system manager sqlite
On some platforms, some of the provided software are not present (generally because we have
not finished porting it). There are sometimes also some specific behaviours or limitations.
On Windows, the Vida IO formats plugins are not present: but we guess nobody cares outside our own lab.
The new fMRI toolbox has not been ported/tested on Windows yet, and is not available.
Mac OS X
Normally everything should work as on Linux, except for
the new fMRI toolbox which has not been ported/tested on Mac yet, and is not available.
Normally everything should work fine on Linux, it is our main development platform.
However you might encounter display problems using 3D viewers based on Anatomist because of
3D graphics cards / drivers / OpenGL issues. See our web site (FAQ and forum) for a bit more information about it.
Support for Sun/Solaris has not been continued since we are not using Solaris anymore.
Support for SGI/Irix has not been continued since we are not using Irix anymore.
BrainVISA can benefit from external software. The software listed here are not
included in the BrainVISA distribution for licencing, or installation, or size reasons
and are not needed to run the core and the main applications. But if they are present on
the system running BrainVISA, some specific processes will be enabled and directly
Moreover some external packages for BrainVISA like the upcoming MEG tools may require
such external software.
Matlab is a commercial product that just can't be distributed freely. If Matlab
is installed, BrainVISA will enable some specific features. It is needed for the
Installation: You may have to set the matlabExecutable variable in the
Preferences menu of BrainVISA, especially if the executable is not just
matlab but something like matlab65.
- The MEG/EEG
package from the
MEG center /
LENA. This package is
not part of our main distrubution, but is available as a separate
- The fMRI toolbox shipped with BrainVISA, which also needs SPM installed.
You can also optionally specify the Matlab release number you are using to help BrainVISA
determine which version of the pymat module to use. If it's not specified, Matlab will be
started to determine its version, so BrainVISA startup will be a bit longer. Note that
matlab release number is not the matlab version number: matlab 6.x is release 12-13,
matlab 7 is release 14.
A link between BrainVISA and SPM is present in BrainVISA for the fMRI toolbox since version 3.1. It is used mainly for the preprocessing steps.
Installation: SPM must be correctly setup in matlab startup paths, or SPM paths must be set in the preferences options of BrainVISA (matlabPath
Other miscelaneous software
Other external software may be used for some processes. Look at the log in BrainVISA to check if some processes are disabled due to missing software. These external software are optional and are used only to provide optional features. For instance, some MPEG encoding software may be used if they are present on the system.
Add-on module packages
BrainVISA is modular, and other people may add new processes for their own tools.
Some labs have made packages and are distributing (or will distribute) them. See the list of available toolboxes on the website : http://brainvisa.info/toolboxes.html
If you have made nice processes for BrainVISA and wish to distribute them as a package,
just tell us (for instance via the forum), and we will
add a link for it on our website.
Our policy is not to include such processes in the core BrainVISA/Anatomist
distribution, but to keep them external and provide some links to them in their home labs. There are two main reasons for this behaviour:
- Preserve the visibility and ownership of package authors: this way external
contributions will not be hidden in the main package: if people want to use the specific
functionalities of an external package, they have to download it from its authors
website, so they know who have made it.
- Avoid the maintenance work for us on these packages