November 18th, 2013, New BrainVISA release: version 4.4.0

This version allows a more incremental management of databases, allowing incremental updates after distributed computing. A new database organization (fully compatible with the previous one) is also provided. Many graphical and practical improvements have also been added, in addition to "traditional" bug fixes. See the Axon detailed changelog.

Anatomist has also undergone some important improvements, in graphical interactions, as well as some new objects types. See Anatomisr detailed changelog

Morphologist provides a reorganized pipeline, and improvements in meshes.

Amongst noticeable changes, the Cortical surface toolbox (LSIS/CNRS, Marseille) has also been significantly improved.

New: (2013/11/18) Vobi One, a new toolbox for functional optical imaging, has just been released by the INT/CRNS in Marseille. See the toolboxes page, or the dedicated web site.

September 6th, 2012 New BrainVISA release: version 4.3.0

In this version, it is possible to store history information about output data generated by Brainvisa processes. History management can be activated for a database through its expert settings activate_history option. History of data can be consulted via the Database browser.

This version also brings a number of bug fixes, and improvements:

February 16th, 2012 bugfix update: version 4.2.1

This version brings a few bug fixes, and improvements:

  • Fix a problem with referentials and transformations in Brainvisa databases.
  • Fix SPM configuration in Brainvisa preferences.
  • Fixes in Soma-workflow integration in Brainvisa.
  • Fixes in Morphologist pipeline.
  • Fix translations in Anatomist.

    • February 3rd, 2012, New BrainVISA release: version 4.2.0

    In this version, it is very easy to do parallel computing in BrainVISA. Indeed, Soma-workflow has now been completely integrated in BrainVisa: processes (pipelines) may be run through a "Run in parallel" button, which allows to dispatch processing across local processors, or on a remote computing resource. A specific GUI allows to control and monitor all executions. Change the user level to Advanced or more in BrainVISA preferences to use this new feature. More information in the BrainVISA manual.

    A new toolbox for Freesurfer is also proposed (user level 1). Some data such as segmentation cortex (ribbon.mgz) can be imported into brainvisa databases and cortical fold graph can be extracted from this freesurfer segmentation.

    This version also brings a number of bug fixes and improvements:

    The package includes Soma-workflow 2.1.

    September 14th, 2011, Bug fix update: version 4.1.1

    This version brings a number of bug fixes, and minor improvements:

    The package includes Soma-workflow 2.0.

    May 17th, 2011, New BrainVISA release: version 4.1.0

    In this version, an important change for the developers should be noted : the build tool used to compile from the source code has changed. We dropped our home-made tool build-config and replaced it with the standard tool CMake, a cross-platform, open-source build system.

    This new package compiled with CMake doesn't need an installation step anymore. You just have to download it and uncompress the archive, then it is ready to use. Thus, there is no setup script or program anymore. The cartopack.sh script that used to add the package paths in environment variables have been renamed into bv_env.sh.

    The package includes a new tool that helps submitting parallel computing to various computing resources: soma-workflow. The documentation is here.

    This version also brings a number of bug fixes, and improvements:

    November 22nd, 2010 bugfix update: version 4.0.2

    This version brings a number of bug fixes, and improvements:

    August 2nd, 2010 bugfix update: version 4.0.1

    This version brings a number of bug fixes, and minor improvements:

    July 22th, 2010, New version of BrainVISA fMRI toolbox : 4.0

    The 4.0 release of the fmri toolbox comprises the following new features:

    It is compatible with BrainVISA 4.0.

    June 15th, 2010, New version 4.0

    This is the first version of BrainVISA using Qt4 API. Be careful, Qt4 API is quite different from Qt3. If some of your own processes use Qt, you may have to port them to Qt4 (See Porting to Qt 4 on Qt documentation pages). This version's source code is still compatible with Qt3, so if you compile from source, you can still use Qt3. Note that the compatibility will not be guaranteed anymore in BrainVISA 4.1.

    This new version also brings a lot of bug fixes and some improvements in user interface:

    January 27, 2010, bugfix update: version 3.2.1

    This version brings, as usual, a number of bug fixes, and minor improvements. A few noticeable changes also:

    November 05, 2009, New BrainVISA release: version 3.2.0

    This new release is mainly due to internal changes and reorganization of our sources repository. This sources repository and web interface for bug tracking are now accessible for open-source parts to contributors. See this page for details.

    This release also brings many bug fixes and improvements :

    July 24, 2009, fMRI toolbox for BrainVISA update: version 3.1.6.1

    This release brings small bug fixes, and introduces python-nifti IO library. More info

    May 19, 2009, fMRI toolbox for BrainVISA update: version 3.1.6

    This release brings brand new group analysis processes. It also corrects some bugs and allows a better gestion of the analysis models. More info

    May 15, 2009, bugfix update: version 3.1.6

    This update brings more bug corrections and improvements. It includes more recent versions of Numpy (1.3.0) and Scipy (0.7.0). The Windows package now uses Python 2.5 like the Linux and MacOs packages.

  • Fixes in BrainVISA: toolboxes can now completely define new ontologies; Suppressed a latency when clicking the "run" button of a process
  • Fixes and improvement in T1MRI toolbox: PrepareSubject process now handles all orientations; new TalairachTransformationFromNormalization process to import orientation parameters from a normalization file...
  • Improvements in Sulci toolbox: new multi-subject sulci snapshot process and new sulci labels transfer process to transfer a labeling to another sulci graph with a different segmentation and graph structure (but same subject)...
  • Fixes and improvements in Anatomist: fix coronal and sagittal views orientation in direct referentials, some objects update functions, "clear unused referentials" feature; new ClippedObject, allowing to cut any object by a clipping plane with its own orientation...

    • March 03, 2009, fMRI toolbox for BrainVISA release: version 3.1

    This toolbox was once a part of the BrainVISA and now is an independant toolbox. More info

    February 20, 2009, bugfix update: version 3.1.5

    This update brings more bug corrections and improvements.

  • Improvement of processes documentation : each data type mentionned in a documentation is a link to a detailed documentation about the data type (inheritance, processes that use it, associated formats, place in Brainvisa databases). The source code of a process can now be displayed in the browser.
  • Bug about process parameters default values.
  • More data types and formats accepted in some processes. Now, it is possible to make the anatomical pipeline generate all the outputs in nifti format for example.
  • Application Qt style can now be changed from BrainVISA configuration panel
  • In databases configuration, ontologies list is not hard-coded anymore
  • Improvement and bug fixes in anatomist python api.
  • A new sulci recognition method is available in BrainVISA : it is faster and behaves differently. It is available as an alternative method in the T1 pipeline.

    • November 14, 2008, bugfix update: version 3.1.4

    This update brings more bug corrections and optimization.

    This package is distributed with the new BrainRAT toolbox dedicated to ex-vivo 3D reconstruction and analysis.

    Starting with BrainVISA 3.1.4, the fMRI toolbox will be distributed separately as a downloadable add-on package to provide it its own visibility.

    October 3, 2008, bugfix update: version 3.1.3

    This update brings more bug corrections and optimization of database access. This package is distributed with a more recent sqlite library.

    September 3, 2008, bugfix update: version 3.1.2

    This update brings more bug corrections, including some database importation problems fixes.

    In Anatomist, a noticeable improvement is the presence of a new gradient palette edition module which may be quite useful.

    August 7, 2008, bugfix update: version 3.1.1

    A number of bugs have been fixed since brainvisa/anatomist 3.1 have been released, so a new package is now available.

    June 9, 2008, new release: version 3.1

    Finally, a new release, after about 3 years of life of version 3.0.x.

    It should work on Linux (Fedora 4 or equivalent and newer distribs), MacOS 10.4 or newer, and Windows XP.

    Amongst the most noticeable changes, we can cite

  • A fMRI module for BrainVISA, partly using Matlab and SPM, on the Linux version only at the moment
  • A new and faster database system in BrainVisa, which will need a conversion of older databases
  • the AimsAlgo part becomes open source (GPL/CeCILL license)
  • A volume rendering module in Anatomist
  • ...

    • May 05, 2006, package update: 3.0.2

    A bugfix update that fixes several problems, especially stability issues on Windows.

    The Mac version now runs on MacOS 10.4 (and not on 10.3 anymore).

    Solaris and Irix versions are still not maintained.

    October 17, 2005, package update: 3.0.1

    A bugfix update that fixes an important bug in the diffusion/tracking algorithms, a number of instabilities (rare crashes) in Anatomist, and adds some "minor" improvements, like multiple matlab versions support in BrainVisa, some optimizations in Anatomist when many complex objects (graphs) are loaded...

    Solaris and Irix versions are still not maintained (the solaris problem might have been solved recently but we need more testing and repackaging).

    June 29, 2005, brand new release: version 3.0 is out

    Finally we managed to release the new version of all of our software. Every project within the package has now version 3.0 (for simplicity).

    This package is released on Linux, Mac OS X and Windows XP systems, and not for Solaris or Irix. This limitation is due to technical problems on our side that may or may not be solved one day. Sorry for this.

    See the release notes and docs for an overview of new features and changes.

    Dec. 2, 2004, stable release update: 2.3.5

    Just after the last update release, we found some bugs in Anatomist display (volume fusions in sagittal slices), and in the Mac version of BrainVisa (and probably the Windows version too), so here is another fix for these problems.

    Nov. 19, 2004, stable release update: 2.3.4

    A bugfix update package (2.3.4) is available in the download section. It fixes some bugs (especially on the Windows version), and includes minor improvements such as matlab support on Windows, SPM2 normalization matrixes importation, and a better installation script. The package should work now when installed in a directory containing space characters.

    Sep. 28, 2004, MacOS X fix update: 2.3.3

    Well, the Mac version has not been maintained very regularly, and I have just noticed that the 2.3.2 binary version has been all messed-up, the distribution is incomplete and out of order. I am sorry about that (but nobody has complained!), the fact is that I didn't have a Mac machine to work on regularly. I have one now (thanks to Jean R�gis, La Timone).

    There is now a new binary package just for Mac, which runs on MacOS 10.3 and without the need of a X11 server, and compiled with optimization on. Be careful, there are still a few problems however:

  • Brainvisa run from the graphical interface of the Mac seems to frequently (and randomly) hang when running commands, so for this version at least, avoid running it by clicking on an icon, but use a terminal... We will investigate this strange phenonemnon when we have a bit of time...
  • This package may not work on MacOS 10.2 and earlier. I have not tried myself, but...

    • Jul. 8, 2004, stable release update: 2.3.2

    Finally we have released a new package (2.3.2) which fixes various bugs encountered in the 2.3 release. Amongst other fixes, we can cite:
  • fix in BrainVisa database hierarchy description which could cause an ambiguity in the anatomical pipeline
  • Fixes in filenames handling when filenames contain space charachers (which often happens on Windows)
  • etc. See individual changelogs accessible via the help pages for more details
    • We do not plan a new version before the end of 2004 because many changes have been started in both BrainVisa and Anatomist and we need time to finish, stablilize and test all the new features.

    Jan. 14, 2004, web server hosting change

    Our website has moved to another place. It is still accessible on its "official" name http://brainvisa.info, but as it used to be just a redirection, your browser has probably bookmarked it as http://brainvisa.free.fr. So please update your bookmarks, the old page will be removed in a short time.
    The new server should be much faster and more reliable, and will allow us to set up a bug tracking tool and a forum and other tools in the future.

    Jan. 6, 2004, MacOS X fix update: 2.3.1

    This is only a MacOS X-specific installation fix: it should overcome the "little squares" syndrom on Anatomist and BrainVisa which do not properly display text on some systems. Basically, I just upgraded some libraries (especially Qt) from the Fink project.
    Jan. 14: Well, no in fact, it doesn't seem to help on MacOS 10.3 - use the trick in the FAQ to get non-antialiased fonts in Qt.

    Dec. 18, 2003, new stable release: 2.3.0

    Featuring BrainVISA 1.6, Anatomist 1.30, Aims 2.13, Vip 2.5 etc.
    At last we are ready to distribute a new version of BrainVISA, Anatomist and all the other tools. Amongst other improvements, we can cite:
  • in BrainVISA:
  • In Anatomist:
  • Many other things which we did not keep track of. A bit more details are available in the different projects changelogs, accessible via the new documentation and help pages
  • And maybe most of all, this is the first stable release to include a Windows version.
    The Windows version is working and nearly fully functional, but there are still some problems in BrainVISA cleanup when exiting, and VIDA and ECAT volume formats are not supported. The other features seem to work well and processings produce the same results as the Unix versions.
    The cache problem of the test releases for Windows is fixed, but at the cost of being slower (possibly MUCH slower for large databases) because BrainVisa must systematically scan every directory when accessing the database.

    • Nov. 16, 2003, one more test package for Windows

  • this pack doesn't use any unix command anymore
  • communication failures between BrainVisa and Anatomist have been fixed (I hope!), after a long and hard fight
  • fixes little things like installation in path containing space characters, ambiguous files naming on case-insensitive filesystems, ...
  • C and C++ sources have been compiled with optimization flags so it may be faster
    • This is still definitely not the final version: there are still problems going on.
  • I have experienced cache update problems with BrainVisa (the cache doesn't update automatically, I have to make a "clearCache" and "updateCache" to make new files visible in the database). We have understood what is going on: Fat32 filesystems don't update directories modification date/time when a new file or directory is created inside it. There should be no problem on NTFS filesystems and on Unix Samba-mounted network drives. We will try to find a workarouond because it is very ennoying, especially when importing a new subject MRI.
  • BrainVisa still doesn't exit cleanly and some temporary files may not be deleted after it exits
    • Oh, by the way, this package has been built on a linux filesystem, so sources (python sources, C++ headers) are in unix ASCII convention. In the counterpart, files which were symbolic links are OK on this version.

    Nov. 04, 2003, another test package for Windows

    This package fixes some problem with the previous one:
  • some missing DLLs and paths in python prevented brainvisa from correctly running commandlines (so almost nothing didn't work!)
  • a bunch of unix-only commands (like rm, cp, mv, touch...) have been removed, but some are still around...
  • a better guess of the home directory is done so that .brainvisa and .anatomist directories may be in a sane place even on other windows than XP

    • Nov. 02, 2003, first development package for Windows

    There are still some problems (Brainvisa exits uncleanly and leaves some temporary files, communications with Anatomist is sometimes lost...) but the main features are working: BrainVisa, Anatomist and the image processing tools are there.
    Some volume IO formats are not supported at the moment: vida and ecat formats are not compiled in the package. These formats require some libraries I don't have on Windows (rpc library).
    But this is one of the last main steps towards the universal portability of the platform...
    This test release is meant essentially for ourselves for debugging purposes, not for end users yet. A new version is planned soon for all platforms (this month if we can take the time to do it).
    Technically, I used the gcc compiler from the MinGW environment, and our configuration tools (build-config/configure/maker) in an unix-like environment (Msys bash shell coming with MinGW).
    Compiling with the gcc compiler from the Cygwin distribution is also possible (and certainly easier in fact), and would allow to build vida and ecat format support because cygwin includes the missing rpc library. But for licensing reasons, we cannot use cygwin: codes compiled with cygwin link against the cygwin DLL which is GPL'd and must be used only for GPL'd code (which is not the case of our algorithms).
    Building with Microsoft C++ compilers (Visual Studio .net) was not possible, the compiler fails on some heavily templated C++ code: don't try the adventure, it's useless.
    The binary distribution contains a copy of the commercial version of Qt library DLL, and of the commercial version of PyQt for Windows.

    May 23, 2003, stable version update: 2.2.3

    Various little fixes (which may be important in some specific cases) in the programs and the package installers, amongst which:
  • Anatomist: fixes in buckets 3D renderings
  • Brainvisa: some problems with parameters links have been fixed
  • MacOS X installer: we used a tar program which was incompatible with Apple's tar, it's fixed now
  • Linux/RedHat9 installer: we switch to the older threading system because the new one causes problems with Python threads
  • Fixes in some lower-level commands: AimsClusterArg, ...

    • Apr. 29, 2003, stable version update: 2.2.2

    A few little fixes (mainly for linux):
  • Anatomist: fixed a crash that could occur while in ROI edition and playing with several volumes with palette windows open
  • Anatomist: fixed the color change of some widgets which does not work with some KDE3 styles (this fix disapeared by mistake in the last stable anatomist release)
  • Anatomist: menu options to save the texture of some textured objects
  • We include again libcrypto and libssl in the linux package since they are required for some python modules

    • Apr. 15, 2003, stable version update: 2.2.1

    This new distribution fixes some installation problems (and offers more precise installation instructions), and fixes a few BrainVisa bugs (the help processes, diffusion package...).

    Apr. 07, 2003, new stable release: 2.2

    A new version of all software has been released, version 2.2 of the pack. Binary packages for Linux (RedHat 7.3 and compatible distribs), Solaris, Irix and MacOS X have been uploaded to the ftp site. See the downloads. We changed the installation procedure: see the .README file with each package. There is now only one file to get, the installer is in it, but you have to unpack it yourself before running the install script.
    It features Anatomist 1.29, Brainvisa 1.5, Aims 2.12, Vip 2.4...
    Main changes: bugfixes (mainly in SPM format IO), many changes in BrainVISA, shfj library is now renamed cartobase

    Feb. 28, 2003, another MacOS X update

    Other little fixes. You may still need to setup the default Qt font using qtconfig. See the FAQ for details

    Feb. 25, 2003: first MacOS X release (development)

    A first development version for Mac/darwin compiled for X11 server. I hope everything is in the package... It has not been thoroughtly tested yet...

    Nov. 08, 2002: new stable release 2.1

    This release is a version upgrade for ALL software: BrainVISA 1.4, Anatomist 1.28, etc.
    Amongst the most important changes:
  • Introduction of functional preprocessing using SPM and Matlab in BrainVISA. This will evolve and more support for higher-level functional processing will be added in futire releases. You must have Matlab and SPM installed to use them.
  • If you wish to build from sources, the gcc-3.x compilers can now be used to build all our C++ code.
    • Binary package notes:
  • This release is the first stable release to provide a binary package for Irix
  • On Linux, we reverted from the behaviour of 2.02-2.04 distribs and we systematically install Qt library again, because there may be system libraries incompatibilities (C++ library), for example on RedHat 8 or Mandrake 9 systems using gcc-3.2. So DON'T USE THE SHFJEnvironmentVariables.sh/.csh scripts in your .cshrc/.bash_profile config scripts ! (or check they are compatible with your system first) - see the FAQ for more details.

    • Sep. 24, 2002: new stable 2.04 release for linux and SuSE-specific development release

    (Installation fix release)
  • 2.04 stable release fixes an installation problem again: home-compiled Qt with good Jpeg support
  • SuSE-8.0 main (devel) release has been made because of system libraries incompatibilities with RedHat

    • Changes between 2.04 and 2.03: Ooops, our Qt lib didn't support jpeg (!)
    Changes between 2.03 and 2.02: installation fix: provide a home-compiled Qt library instead of RedHat's customized one, and install it only if the target system doesn't already have it

    Aug. 22, 2002: first complete binary package for Irix

    An Irix package is now available (development version) and contains the full set of programs and libraries: brainvisa, anatomist and all tools

    09/08/2002: new stable release 2.02

    Featuring Anatomist 1.27, BrainVISA 1.3 etc.
    Changes between 2.02 and 2.01: installation bug fixes
    Changes between 2.01 and 2.0: fixed a few broken functionalities in Anatomist 1.27 and some low-level Aims commands