BrainVISA software Download

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Release:4.6.1

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

Download

Binaries

version

OS Online Size Online md5 Offline Size Offline md5 Repository

Warning

Mac packages are broken

2018/03/09

The Mac packages 4.6.0 are currently broken, due to a bug in our packaging program. We are fixing it ASAP. Sorry...

The installation process runs into errors, complaining about memory issues (which is not the real problem). It is possible to skip the affected packages, but the installation will be incomplete.

The affected packages are axon (brainvisa program) and all toolobxes. Anatomist should run, except for the run script in the root of the installation directory. You have to use bin/anatomist instead for now.

Note

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.

Note

Problems with the Windows version: Fixed.

Release 4.5.0 for Windows had an unstability problem. The newer version 4.6 should solve this.

Sources

Older releases

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

version

OS Online Size Online md5 Offline Size Offline md5 Repository

Installation

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

Running on Windows 10 + Ubuntu shell

It is also possible to use the Linux version of BrainVISA on Windows 10 using the Ubuntu Windows Subsystem for Linuw (WSL). Here are the instructions, as reported by one of our users (thanks François Tadel):

  1. In Windows 10: Enable WSL and Ubuntu, there are many online tutorials available for that, for example: https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/

  2. In Windows 10: Install the free version of MobaXterm: https://mobaxterm.mobatek.net/

  3. In MobaXterm: Menu Settings > Configuration > tab X11:

    • Xorg version: Cygwin_1.16.3
    • OpenGL acceleration: Software
  4. In MobaXterm: Menu Sessions > New session > tab Shell > Terminal "Ubuntu bash (WSL)" > OK

  5. In MobaXterm: In the session lists, select the new “Ubuntu Bash” session

  6. In bash terminal: type:

    sudo apt-get update && sudo apt-get dist-upgrade
    

    to upgrade all the packages in Ubuntu

  7. In the bash terminal: type:

    export DISPLAY=:0
    

    to send the X11 windows to the local MobaXterm X server (add this line to your .bashrc to save time in the future)

  8. In the bash terminal: Type firefox, then download and install BrainVISA for Ubuntu 16.04.

  9. In bash terminal: Remove the BrainVISA version of libxcb to avoid the errors "libxcb-dri3.so.0: undefined symbol: xcb_send_fd":

    rm brainvisa-4.6.0/lib/libxcb*
    
  10. In bash terminal: If you have additional errors, you may also try removing the BrainVISA version of libgcc_s, libpcre, libstdc++, libtinfo (you may have to install these packages manually):

    sudo apt install gcc g++ libtinfo-dev libpcre++-dev
    

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.

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

Licences

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 http://www.cecill.info/index.en.html

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.

Troubleshooting

Error message /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0: undefined symbol: xcb_send_fd
If you see this message your system needs a more recent libxcb library than the one provided in the BrainVISA package. To fix this, you can either try another BrainVISA package build on a more recent system (see the glibc version on the package name) or remove all the files starting with libxcb from the lib directory of the BrainVISA package.