BrainVISA software Download


BrainVISA is a set of software, freely distributed as software bundles for Linux, Mac and Windows.




OS Online Size Online md5 Offline Size Offline md5 Repository


Problems with the Windows version

Release 4.5.0 for Windows has an unstability problem that we could not solve at the moment: Anatomist seems to hang randomly in some dialog boxes or when quitting the application. On some systems (Windows 10) it has been reported to crash or freeze when using the “open file” dialog, which is of course very annoying. We are still investigating the problem, but have not found the cause for the problem yet. So use it with care, and be aware of the problem. An update will be released when we find a solution for it.

Meanwhile, you can still use a Linux version in a virtual machine, if needed.


Online and Offline installers

You normally need the “online” installer variants, which are more lightweight: they will download packages which need to be installed, and only them, once they are selected. The “offline” installers contain all the builtin packages, and thus do not need to download them when installing. Use them to install BrainVISA on computers which cannot access the internet network.


Older releases

Version 4.5 or newer: New modular installer
Version 4.4.0 or older: single monolithic archive


  • Download the installer program for your operating system. Choose the appropriate online / offline installer (see above)
  • Run it
  • follow the instructions to select the installation directory
  • follow the instructions to select the desired packages to install

You will need a network connection during installation when using the “online” installers.

  • Three main programs, BrainVISA, anatomist, and morphologist are available directly in the root directory of the installed software.
  • A lot of other programs are located in the bin subdirectory.

Note that packages repositories may be configured in the installation program, and additional repositories may be added, for instance to include packages maintained by external labs.

Once installed, the setup program BrainVISA_Suite-Update will allow to update some packages, install new ones, or to setup additional repositories.

Getting started

Three main programs, BrainVISA, anatomist, and morphologist are available directly in the root directory of the installed software. A lot of other programs are located in the bin subdirectory.

anatomist is the interactive 3D visualization software.

morphologist is the new user interface for the main Morphologist pipeline.

brainvisa is the user interface to Axon, which will generally be the entry point to all other applications and toolboxes. You may also have access to morphologist and anatomist from the brainvisa program.

Once started, brainvisa will need a bit of configuration: go to the “BrainVISA / Preferences” menu, and setup especially paths to external software such as Matlab, SPM, FSL or Freesurfer if you have installed them.

BrainVISA is working with files and directories organizations, and local databases, more generally regrouped under the term “databases”. You will have to setup at least one to make it work in optimal conditions. At the beginning a database is a new, empty directory, where BrainVISA will import unprocessed data and write processed data.

Before running processing, raw data thus has to be imported in such a database: use the “Data management” tools, “import” to do so. For T1 MRI processing (using Morphologist), you will typically use the “Import T1 MRI” process, or the “Import DICOM T1 MRI” process. Appropriate import processes are generally also found in processing toolboxes.


More information may be found in the Axon tutorial and, more generally in the Axon documentation.


Globally, it is free for a non-profit usage.

As the whole set of software contains several sub-packages, each may have its specific licencing policy. See individual modules for licence information.

Some are “really” free and open source (CeCILL-B, BSD-like licence), some are CeCILL-v2 (GPL-compatible), and some are closed source with free binary distribution for non-profit usage.

The core is as free as possible: CeCILL-B when possible, or CeCILL-v2 when using PyQt which is GPL:

  • Axon is CeCILL-v2
  • Anatomist is CeCILL-B, with some additional python plugins which are bound to GPL.
  • AIMS (image processing tools) is CeCILL-B

CeCILL licences are compatible with their GPL or BSD equivalent, but with additional legal precisions for french laws. See

This basically leaves the possibility for toolboxes developers to choose the licence which suits them (open or closed), with some PyQt (GUI) parts which have to be GPL-compatible.

  • Morphologist, BrainRAT, cortical_surface and some other toolboxes also include closed-source code in their algorithmic parts. They can be used freely for non-profit usage.
    • Typically academic research applications are OK.
    • Commercial applications of these toolboxes should contact their authors before proceeding.