BrainVISA Changelog

Changes history in BrainVISA


Axon changelog

Anatomist changelog

Aims changelog

March 2023, new BrainVISA release: 5.1.1

Bug-fix and minor imprivements release:

  • Fixes and improvements under the hood in AIMS / PyAIMS libraries.

  • Possible crash in sulci deep CNN recognition fixed.

  • Fixes in Anatomist colormaps tables handling.

  • Brainvisa switches back to using an older API to display HTML docs because it could cause crashes on old linux systems (even inside a container)

January 2023, new BrainVISA release: 5.1.0

  • This containerized release is based on an Ubuntu 22.04 system, and compiled for Python 3.10 and Qt 5. This is thus the first official binary release based on Python3 (yes, finally…)

  • It also ships a copy of SPM12-standalone, preconfigured in Axon (brainvisa) in order to work out-of-the-box without user configuration.

  • Towards BIDS compatibility: Morphologist (in Axon and Capsul) can now support a new BIDS-compatible ontology. The Freesurfer toolbox also supports a new BIDS-like ontology.

  • Several significant news in Anatomist, see Anatomist changelog

  • The image processing libraries (AIMS/PyAIMS) have been cleaned from some obsolete data structure, and improved in several ways. Some old commands (Vip) have also been removed when existing in a newer shape.

  • Very important performance improvements in Soma-Workflow, the parallel execution tool.

  • The SnapBase tool, which had not been maintained for years, has been removed.

  • Morphologist: the CNN sulci recognition could produce (in rare bad cases) both sulcus vertices with disconnected voxels, and adjacent cut vertices with the same label (which was not severe but useless). This has been reworked and fixed. As a consequence, the outputs of CNN sulci recognition are different in 5.1 and 5.0.

  • Minor improvements, and many fixes in both infrastructure and toolboxes.

December 2021, new BrainVISA release: 5.0.4

Bug-fix release:

  • various fixes in aims, anatomist, axon, capsul…

  • fixed brainvisa (axon) docs not present in 5.0.3 packages

  • Fixed use of libjxr in Openslide format support

October 2021, new BrainVISA release: 5.0.3

Bug-fix release:

  • Fixes in Aims libraries (Mesher, AimsRegisterFFDEstimate, AimsTex2Vol)

  • Minor improvements in aims docs

  • Fixes in Anatomist: crash in Fusion3D using more than 2 volumes, folds split, CutMesh referentials issue, …

  • Detailed doc about palettes and texturing in Anatomist

  • Fixed processes doc given in axon-runprocess

June 2021, new BrainVISA release: 5.0.2

Fixes for the following issues:

  • unable to read Nifti files whose name is shorter than 7 characters.

  • all commands fail to start with nvidia-container-cli: initialization error: nvml error: driver not loaded.

  • Spurious ‘s in BrainVISA process documentations

  • aimsalgo.resampleBucket() has a bug

  • Uncatched exceptions that occurs in BrainVISA lead to a crash of the application

  • Missing includes dependency in Makefiles

  • Opening Graph file by clicking the “eye” button crashes BrainVISA

  • returns all-NaN transformation matrices

March 2021, new BrainVISA release: 5.0.1

  • Small improvements and fixes

January 2021, new BrainVISA release: 5.0.0

  • Brings a new installation method as virtual containers or virtual machines.

  • Morphologist sulci identification is using a new method (based on deep learning CNNs)

  • Many smaller improvements and fixes

September 2018, BrainVISA bugfix update: version 4.6.1

Fixes a number of issues, including the broken Mac package. Most other are relatively small fixes and improvements.

  • Anatomist:

    • Allow to put independently several volumes in the same window: a fusion will be created on-the-fly

    • New little image “math” module

The Constellation toolbox has still not been finished for this release.

Febuary 2018, new BrainVISA release: version 4.6.0

  • General:

    • Windows version has been fixed

    • Windows 64 bits version

    • Stopped the Fedora-4 32 bits version. All linux builds are in 64 bits.

  • Anatomist:

    • Supports object of any dimensionality (not limited to 4D any longer)

    • Partial support for CIFTI connectivity matrices

    • New referentials window, rewritten in 3D

    • Windows snapshots of any dimension, rendered off-screen

    • Save/reload fusion objects and multiple objects (.aobj format)

    • Display normals of a mesh

    • Display vector fields

    • Many other fixes and smaller improvements

  • New project: Primatologist Which is part of the BrainRat project from Mircen BioPicsel lab.

  • Coming soon

    • Constellation, the connectivity-based parcellation toolbox for BrainVisa, is still a bit delayed because of recent changes, and to allow us to ship an atlas with it. We hope it will be released soon, before a full new brainvisa release.

    • Highres-Cortex, See the doc. As for

    Constellation the release will be delayed a little bit.

  • Removed obsolete toolbox Connectomist-1

    This toolbox was almost unmaintained for about 10 years. Parts still useful have been integrated in the AIMS library, and in Constellation

  • Notably nothing important in Morphologist… a few minor improvements in morphologist UI

  • For developers:

    • Ported all libraries to Qt5 or Qt4

    • Support for python3 in a subset of projects (noticeably excluding Axon)

    • Support for C++11 in all C++ libraries, also compiles using LLVM compiler

    • Capsul has notably improved and matured, integration in Axon has also improved (although it is not entirely integrated yet)

    • New development and build system in Docker containers: casa-distro project

Febuary 2016, new BrainVISA release: version 4.5.0

  • Morphologist:

    • Imporoved meshes.

    • Additional optional step to skull-strip the brain and use it in a second normalization step, to improve alignment robustness.

    • A variant of the pipeline is the premise to the future redesigned pipelining system (Capsul): “Morphologist CAPSUL iteration”. It should behave the same way, but preparing a large iteration on many subjects should be more efficient and faster. The process produces a workflow, to be run in soma_workflow_gui

  • Morphologist UI: a new simplified interface to the Morphologist pipeline. See the documentation

  • Cortical_surface:

    • New sulcus parameterization, faster, more robust, better properties.

    • Improved version of the Hip-Hop cortical parameterization process

    • The MarsAtlas cortical parcellation model has arrived !

    • Sulcal pits computation for individual subjects.See in Anatomy section.

    • The Depth Potential Function (DPF) computation is now included in the Anatomy / tools section

  • Anatomist:

    • Supports Wavefront .obj format

    • Supports NIFTI-2 format

    • Supports Trackvis .trk format

    • Can save and reload textured meshes with colormap (as .obj), especially convenient to import/export with other software like Blender.

    • Shader-based rendering of fibers, with coloring

    • Major improvements in SurfPaint module

    • Improvements in transparent objects rendering (possibility to sort polygons)

Anatomist/BrainVISA changelog

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:

  • BrainVISA (See detailed changelog)

    • Information message when a new version of Brainvisa is available on
    • Invalid processes are not hidden anymore
    • The documentation panel in Brainvisa main window is now a real web browser.
    • Reusable Anatomist windows in Brainvisa
    • New feature in menu View -> Close all viewers
    • Important changes for developers:

      • Anatomist in "direct" mode: this change allows more sophisticated viewers (BV/Anatomist combined interfaces)
      • Reorganization of Brainvisa python modules
    • Morphologist toolbox

      • The T1 MRI, Sulci and Morphometry toolboxes are now grouped together into the Morphologist toolbox.
      • Snapbase: a new tool to do large scale snapshots of data from Brainvisa databases.
      • Fix an incorrect flip in Prepare subject step in a specific orientation.
  • Anatomist (See detailed changelog)

    • New 2D fusion modes
    • Fix visibility of icons in menus
    • Fix closing mode in ROI toolbox
    • Fix to enable displaying huge images
    • The Clear everything menu can really close all windows now
    • The matplotlib-histogram window has been improved, and is now the default histogram window
    • The manual sulci splitting plugin has been significantly improved
    • Graph labels display as text in 3D
    • Anatomist windows highlighting
    • Optimizations in huge nomenclature / graphs coloring
    • Use the Qt4 file dialog
  • Aims (See detailed changelog)

    • AimsVoiStat command is now deprecated, AimsRoiFeatures command should be used instead
    • It is now possible to use volumes whose size is larger than 32 bits.
    • Fix in AimsFoldArgAtt command
    • Fix in fold split
    • Fix operators on volumes in PyAims

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:

    • BrainVISA (See detailed changelog)
      • GUI changes in BrainVisa main window
      • Transformations manager performance improvements
      • "Reload toolboxes" option in BrainVISA menu
      • Processes and iterations numbering improvement
      • New data lock feature
      • New process InspectMultipleData in data management
      • Fixed environment variables when using external commands from brainvisa.
      • Fixes in file selection of a list of output files.
      • T1 MRI toolbox
        • Support for SPM8 and SPM8 compiled version for normalization process
        • Hemisphere and white meshes are now more accurate, prettier, and conform to the spherical topology constraint.
        • SPM and FSL normalization processes can retry after a failure due to a bad initialization
      • Sulci toolbox
        • SPAM sulci recognition models data have been reorganized.
        • SPAM models viewers have been improved and a bad interaction with other objects in anatomist has been fixed.
      • FreeSurfer toolbox
        • A process to import the freesurfer segmentation (ribbon.mgz) and to extract cortical fold graph from this segmentation (and not this computed by Morphologist pipeline (user level 1).
        • Many processes under development in user level 2. These processes are unstable, so if you want to try them, please remenber that ...
    • Anatomist (See detailed changelog)
      • Box selection highligting feature
      • Fixes and improvements in browser window
      • Windows blocks improvements
      • New config option: commonScannerBasedReferential. When enabled, all such referentials found in image headers are assumed to be the same.
      • Surfpaint module update
      • New palettes: "Graph-Label", "pastel-256", "French"
      • Fixes and improvements about referentials and transformations
      • Fixed multi-texturing bug on Windows OS
    • Aims (See detailed changelog)
      • Geodesicpath library update
      • DICOM reader fixes for a few header fields, and support for SPECT data.
      • Fixed rescaling in volume converters
      • Fixed a bug in SplineResampler

    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:

    • BrainVISA
      • Updated tutorial available
      • Fix the field "defined in file" in the Brainvisa ontology documentation.
      • Brainvisa Python API documentation in sphinx format available.
      • New supported mesh format: MNI .obj
      • Fix generic importation of a graph in basic user level mode.
      • Fix concurrent creation of a directory in case of parallel executions of Brainvisa.
      • New python module to start Brainvisa in batch mode: brainvisa.axon.
    • Anatomist
      • New rotation mode where we don't need to keep the middle mouse button down: it is now possible to rotate an object by performing a double click with the middle button and moving the mouse. Another click ends this special rotating mode.
      • New Text objects to display text information in Anatomist windows.
      • More python bindings in the Python API.
    • Morphologist toolbox
      • Fix missing step in graph upgrade process.
      • Fix wrong link in Cortical fols graph process.
      • Fix a bug in the closing option of VipGetHead command.

    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 script that used to add the package paths in environment variables have been renamed into

    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:

    • BrainVISA
      • Text search available in the log throught ctrl+F and F3 keys
      • Text viewer available for more data types (csv, xml files).
      • [programmers] Brainvisa now uses sip QString API version 2, so it not possible to use QString and QStringList classes anymore, python types should be used instead.
      • Fix graphviz packaging which make generation of ontology documentation with types inheritance graphs available.
      • Update in programming documentation about GUI customization
      • T1 MRI toolbox
        • New T1 pipeline named Morphologist. This new version is more robust and efficient.
        • T1 Normalization processes (using FSL or SPM) have been moved from fMRI to T1MRI toolbox. So, it is now possible to choose normalization instead of manual localization of AC/PC in the anatomical pipeline without having the fMRI toolbox installed.
      • Sulci toolbox
        • New process SPAM models installation to install SPAM models for sulci recognition. The installation of the required models is checked in the Morphologist pipeline.
        • Add new 2011 ANN models to sulci recognition available models. These models implement the older method, on the same (newer) learning database as the one used for SPAM models.
        • Bug fix in iterative mode of a sulci graph viewer
      • BrainRAT toolbox
        • Add RGB/RGBA background estimation to subsampling and to intra volume registration process
        • Add advanced slice replacement process
    • Anatomist
      • New surfacic ROI drawing toolbox: it is now possible to paint on a mesh (into a texture), and use curve drawing tools which include curvature constraints. This toolbox is developed in Marseille by O. Coulon's team, mainly by A. Le Troter.
      • Update and additions to pyanatomist documentation.
      • Bug fix in FusionRGBAVolumeMethod fusion method
      • Bug fix in palette update in a MultiTexture fusion
    • Aims
      • Add support for RGB/RGBA background in AimsResample
      • PyAims
        • Bug fix in aims.write when the specified path doesn't exist.
        • Helper functions to create the main Aims data types
        • Allow additional constructors arguments for volumes and textures (build from another volume, or a numpy array...)
        • Big fix in TimeSurface erase function

    November 22nd, 2010 bugfix update: version 4.0.2

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

    • BrainVISA
      • New progress bar in processes and pipeline windows.
      • Viewers and Editors are now available for list of data. The default viewer is an iteration of the viewer for the type of data in the list.
      • Fix background and foreground color of choice nodes in pipeline graphical interface.
      • Fix iteration on Series of 3D volume (Import fMRI data)
      • Database browser: enable visualization of unrecognized data if a viewer that accepts the data format exists.
      • Fix commands log in windows version.
      • Documentation panel : enable links with anchor and open web links in a real web browser when possible.
      • Browse button in process iteration dialog always opens the dialog that enables selecting several files at different location on the filesystem. This action was only available through right click before.
      • Improvement of database update when a process finishes : intermediate directory items created by the process are inserted in the database; output parameters of a sub-process not in a pipeline are inserted in the database.
      • Improvement in Morphometry statistics process : output parameters are now output_directory and output_filename_prefix instead of output_prefix and have default values.
      • Improvement in DicomToNiftiConverter process : enable choosing the output filename and giving a directory containing dicom images instead of a file as input parameter.
      • New importation process to import a T1 MRI from a Dicom directory using Mricron Dicom converter.
      • Fix Single file to serie process : generate the numbers of the serie with a fix number of digit to ensure that the files of the serie are in the correct order.
      • T1 MRI : new sulci voronoi step before the folds thickness step, to allow saving and reusing the sulci voronoi maps; New type for lesion mask used in the brain segmentation parameters.
      • Sulci : new processes to calculate the mean distance from a lesion mask to sulci.
    • Anatomist
      • New option in Anatomist config and preferences panel: clipBrowserValues. This option allows to limit the size of strings displayed in browsers attributes, and avoid crashes due (probably) to too large pixmaps in X servers in some specific cases.
      • Gradient palette available for RGB images.
      • Improvement of tooltips on graphs in "display property" mode
      • Fix rendering problems using ATI cards and drivers on S16 volumes.
      • Fix ROI cursor display
    • Aims
      • Fix reading GIFTI files extracted from SPM 8 and GIFTI mesh+texture files
      • Fix reading and writing transformations in MINC format
      • Support for MNI .obj mesh format
      • Forbids to write NIFTI format when volume dimensions do not fit in short ints: NIFTI stores dimensions as short.
      • New option in AimsFileConvert: --orient, to specify output disk orientation or flip it
      • AimsFoldGraphThickness can now use a pre-built sulci voronoi map (to speed things up)
      • AimsLabelSelector can now work in batch mode (-b) without graphical interface.

    August 2nd, 2010 bugfix update: version 4.0.1

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

    • New Dicom converter using Mricron. The converter is in toolbox tools -> converters. It is available if Mricron is installed on your computer.
    • Fix database conversion process which was not compatible with qt4.
    • Fix BrainVISA log file.
    • Cortical surface: Fix gyral parcellation (command siParcellation).
    • T1 MRI pipeline: test if brain mask is empty or full and fail accordingly
    • Sulci: Fix scripts siCSVMapGraph, siDiffModels, siDisplayGraph and annealing_tag which were not compatible with qt4.
    • Anatomist: graph labels picking/copy/paste from one window to another is now possible.
    • BrainRAT:
      • Fix issue in intra volume propagative slice registration
      • Fix command AimsFFDApply
      • Add AimsFlip RGB support
      • Add a variation ratio parameter to AimsIndividSlices
      • Add RGB support to FlipApplication
      • Add threshold parameter to IntraVolumePropagativeSliceRegistration process
      • Fix issue in AimsIndividStackSlices and AimsIndividSlices

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

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

    • Improved and more robust cortical surface-based analysis procedures.
    • Improvements in multi-subjects analysis, such as the introduction of second-level design matrices.
    • Better integration of General Linear Model in the volume and on the surface with high-level operations (group analysis, reproducibilitry assessement, parcellation and functional landmark characterization).

    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:

    • BrainVISA
      • New contextual menu on pipelines and iterations enabling easy selection, deselection, opening and documentation display of the different steps.
      • Visual feedback in processes graphical interface to show which parameters have been modified.
      • BrainVISA documentation panel: keyboard shortcuts for contextual menu items and a new button to reload the current documentation page.
      • Attributes sorting enabled in database search interface (available only in Qt4 version).
      • Import T1 MRI: the default value for subject attribute is the name of the file.
      • Types and formats documentation now shows the hierarchy rules for all available ontologies
      • Fix: parameter exactType in WriteDiskItem initialization is now taken into account.
      • Sulci toolbox - ergonomy improvements in Sulci recognition pipeline: combo boxes to select the recognition method.
    • Anatomist
      • OpenGL-based selection infrastructure. Selection functions for meshes and polygons have been included in Anatomist. In "debugger" mode (userLevel >= 3) this mode replaces the older graph/bucket selection mechanism. When correctly tested, it will fully replace it.
        A little texture drawing code example is now part of the examples.
        The new infrastructure is not optimized at all yet, so, drawing is slow, but we will improve it in time to avoid unnecessary OpenGL renderings.
      • Python bindings and the python API have been slightly improved.
      • New command: ApplyBuiltinReferential
      • The file browser for loading objects now shows all file extensions used by supported objects files. Extensions list is built dynamically from the loaded readers.
      • Clearer tooltips in the referentials window.
      • Many problems have been fixed when Anatomist is built using Qt4. Some modules had not been ported or tested, and Mac and Windows ports had not been tried. Now things are mostly tested.
    • AIMS
      • Improvements and fixes in various IO modules: Dicom, Nifti, Gifti, FDF
      • Beginning of a SQL database format for graphs (QSlite files for now). This will allow partial reading and queries in large graphs databases. But the module is still experimental and the SQL database schema will probably change, so it should not be used yet to store important graphs. Conversion from and to the .arg format are still possible.

    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:

    • Binary packages
      • Something we just forgot to mention but was already present in version 3.2: Linux packages include a software OpenGL library (Mesa) which may be used in place of the system one in case of 3D drivers rendering problems. To enable it, just move the files in <cartopack_directory>/lib/mesa/ into <cartopack_directory>/lib/ and re-run Anatomist/BrainVisa. It is slow because it does not make use of the 3D hardware at all, but should work and display correctly in all cases. Only use it if the system OpenGL does not work well.
      • A few system libraries have been added to the binary distribution to overcome compatibility problems on some systems.
      • The fMRI toolbox will also be released for the Linux Mandriva 2008 x86_64 (64 bits) version.
    • BrainVISA
      • A serious bug has been fixed on the database system on Windows, it fully made the database unusable in 3.2 version (on Windows). It is now fixed.
      • T1 pipeline: the pipeline can now make use of the spatial normalization processes of the fMRI toolbox to replace the manual AC/PC clicking step. To make it available, you need to have the fMRI toolbox installed, and also have either FSL or SPM5 (+ Matlab) installed and present in the PATH. As the fMRI toolbox is only released for Linux, you will not be able to have it on Mac and Windows (unless you install the sources of the toolbox, actually at least the FSL normalization does work on Mac).
      • Sulci recognition: The various and more advanced sulci recognition methods of Matthieu Perrot's PhD work have now been released. They need to install additional models archives. See the docs of the SPAM-based recognition processes.
      • A few little improvements to make database and T1 import processes more practical.
    • Anatomist
      • A new simplified viewer application has been developed: It offers a simple and easy interface in a single window using a fixed 4-views layout, which is more classical and more convenient for inexperienced users. It is a restricted and constrained use of Anatomist capabilities. It has been developed in a few nights, at first to show that developing simple custom applications using Anatomist libraries is not so difficult and may be done quite fast in Python language...
      • A new plugin allows to tune the palette (contrasts) of objects using the mouse right button (+ shift/control keys) directly on 2D/3D views without opening the palette window.
      • A better histogram window plugin, based on Matplotlib, which offers interactivity (zooming, saving/snapshot in either bitmap or vector formats, ...)
      • The ROI drawing cursor hs been fixed and re-activated on Mac

    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 :

    • Binary Packages
      • The windows version should work on Windows Vista.
      • A 64 bits binary package is now available for Linux.
      • The Mac version is now built on an Intel machine. It is no longer compatible with PPC processors, but it should run way faster on Intel Macs.
    • BrainVISA
      • Several improvements on BrainVISA databases :
        • Optimization of databases requests. The results are now shown as a table of attributes values.
        • Easier database request with existing values of databases attributes selectable
        • Databases can be moved without needing update.
      • DiskItem selection window cannot become higher than screen anymore
      • No more useless *.minf created by processes
      • Iteration control : it is possible to stop the current iteration or all iterations.
    • Anatomist
      • VTK plugin by Pierre Fillard, which allows to render VTK objects, and especially enables a mix between Anatomist and MedInria objects.
      • GIFTI format IO support for meshes and textures

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

    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, but as it used to be just a redirection, your browser has probably bookmarked it as 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:
    • easier database setup which can now be done via the menus
    • some improvements in the user interaction and viewers
    • mproved (althrough still not complete) help system
    • working diffusion / fiber tracking pipeline
  • In Anatomist:
    • minor GUI improvements: viewing images in radio or neuro convention, new setup options, visibility or usability comfort improvements
    • new functionalities in the ROI drawing module (morphological math operations...)
    • fixes and improvements in several volume formats IO...
  • 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 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