BrainVISA ChangeLog



Version 5.0.0
Version 4.6.0
Version 4.5.1
Version 4.5.0
Version 4.4.0
Version 4.3.0
Version 4.2.1
Version 4.2.0
Version 4.1.1
Version 4.1.0
Version 4.0.2
Version 4.0.1
Version 4.0.0
Version 3.2.1
Version 3.2.0
Version 3.1.6
Version 3.1.5
Version 3.1.4
Version 3.1.3
Version 3.1.2
Version 3.1.1
Version 3.1.0
Version 3.0.2
Version 3.0.1
Version 3.0.0
Version 2.3.5
Version 2.3.4
Version 2.3.2
Version 2.3.0
Version 1.5

2021/01/20 - Version 5.0.0

2018/02/05 - Version 4.6.0

2017/01/01 - Version 4.5.1

General bug fixes and improvements:

Developers-oriented:

2016/02/17 - Version 4.5.0

General bug fixes and improvements:

2013/09/09 - Version 4.4.0

General bug fixes and improvements:

General processes:

Morphologist toolbox:

2012/09/06 - Version 4.3.0

General bug fixes and improvements:

2012/02/16 - Version 4.2.1

General bug fixes and improvements:

2012/02/03 - Version 4.2.0

General bug fixes and improvements:

2011/09/14 - Version 4.1.1

General bug fixes and improvements:

Version 4.1.0 (2011/05/17)

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 gave up our home-made tool build-config and replace it with the standard tool CMake, a cross-platform, open-source build system.

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

Version 4.0.2

General bug fixes and improvements:

Version 4.0.1

General bug fixes and improvements:

Version 4.0.0

Version 3.2.1

General bug fixes and improvements:

Version 3.2.0

  • BrainVISA package should work on Windows Vista
  • Databases are not automatically updated anymore. It is always asked to the user before.
  • 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.
  • Several other bug fixes
  • Version 3.1.6

    General bug fixes and improvements:

  • Toolboxes can now completely define new ontologies
  • Some parameters links fixes and improvements
  • Suppressed a latency when clicking the "run" button of a process
  • Fix: some attributes in output disk items browser were erroneously hidden, which actually made it impossible to write some specific data types.
  • Fixed synchonization problem between database content and minf files content, which could cause strange problems when re-processing or re-importing data over existing older ones
  • Several other bug fixes
  • Toolboxes:

  • Fixes in animation/mpeg processes
  • SPM normalization files conversion has been re-written, and can handle SPM5 and SPM8 files
  • T1: the reorientation routines in PrepareSubject have been re-written. They now handle any orientation
  • T1: new TalairachTransformationFromNormalization process, to import orientation parameters from a normalization file
  • T1: fixes in some memory (re-)allocation functions on Mac, which caused memory consumption to grow anormally and some commands to crash in the T1 pipeline.
  • T1: fixes in 3.1 graphs: on sulcus opening descriptors, which mixed unnormalized CSF volume and normalized sulcus surface, on grey_surface_area, and on cortical thickness which could be inaccurate in some locations (sulci fundi especially)
  • T1: in 3.1 graphs construction or upgrade variants, the process crashed on Windows. We fixed it by disabling multithreading on Windows, and making it optional on other platforms.
  • T1: set total sulci length in global graph attributes of 3.1 sulci graphs
  • Sulci: new multi-subject sulci snapshot process
  • Sulci: new sulci labels transfer process, to transfer a labeling to another sulci graph with a different segmentation and graph structure (but same subject)
  • Version 3.1.5

    General bug fixes and improvements:

  • Improvement of processes documentation : each data type mentionned in a documentation is a link to a detailled 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.
  • Application Qt style can now be changed from BrainVISA configuration panel
  • In databases configuration, ontologies list is not hard-coded anymore
  • Improvements in pipelines remote execution
  • ... and many other fixes and improvements under the scene...
  • Version 3.1.4 (14/11/2008)

    General bug fixes and improvements:

  • Bug when a BrainVISA database is not available.
  • Bug in database conversion process with sulci directory.
  • Improvement of ListOf parameters management.
  • Possibility to import a T1 MRI in NIFTI format.
  • Improvement of the generic importation process.
  • New process in tools -> documentation to generate documentation about BrainVISA types.
  • ... and many other fixes and improvements under the scene...
  • Toolboxes :

  • BrainRAT toolbox is now distributed with BrainVISA.
  • The fMRI toolbox will be distributed separately as a downloadable add-on package to provide it its own visibility.
  • Version 3.1.3

    General bug fixes:

  • More database fixes: especially, optilization issues were fixed, which made acces very slow (especially on a network) and going slower and slower while working in a brainvisa session.
  • The database access interface (database buttons on processes parameters) has been improved, especially for output values: it is now possible to type lists of editable attributes, making it possible to iterate importation processes for instance (iterate to import 3 files, just type 3 subjects names).
  • The "save process" (.bvproc files) feature now also works on iterations. Warning: The structure of bvproc files have changed: new files will not be readable by older versions of Brainvisa.
  • Iteration parameters inputs are a bit smarter and a bit more convivial: parameters with a single value are interpreted as the same value for all iterations.
  • Improvements and customizations in database conversion processes, especially when dealing with unrecognized data.
  • in the T1 pipeline, the newer cortical folds graph creation/upgrade processes have been fixed and optimized: the cortical thickness calculations don't take hours anymore.
  • ... and many other fixes and improvements under the scene...
  • Version 3.1.2

    General bug fixes:

  • Some database fixes
  • Several other little things...
  • Version 3.1.1

    General bug fixes:

  • Fixed some importation processes
  • Fixes in database update
  • Fixes in database conversions (3.0 to 3.1) when converting "dirty" databases
  • Fix: in some conditions, user typed values in processes GUI where not taken into account
  • Many less important little fixes
  • Version 3.1

    Core:

  • New organization of BrainVISA processes toolboxes. Each toolbox can define its own processes, extend database ontology, extend BrainVISA GUI (for instance add specific entry in preferences window), etc. A new panel has been added to BrainVISA main window to select toolboxes.
  • BrainVISA user directory ($HOME/.brainvisa under Linux and Mac and most often C:\Documents and settings\{user name}\ under Windows) is now considered as a toolbox named 'My processes'.
  • New preferences panel with a tab for each group of options. Options are now saved in options.minf in BrainVISA user directory.
  • It is now possible to add custom processes trees in the main window (saved in userProcessTrees.minf in BrainVISA user directory).
  • Database system had been rewritten for better performance and scalability. The new system is based on SQLite.
  • Default databases organization had been modified. Old organization (named brainvisa-3.0) is not compatible with new brainvisa-3.1.0 organization. A converter had been written to convert from brainvisa-3.0 to brainvisa-3.1.0.
  • Added support for NIfTI-1 format.
  • An experimental framework for distribution of processes on several computers had been released.
  • The Python API to control Anatomist from Python had been completely rewritten (and documented).
  • Management of referentials and transformations had been improved.
  • New features in process Database Hierarchy Browser: it is possible to search data, copy data using drag and drop, call a viewer, remove data, and convert graphs (using process Compute Cortical Fold Graph Upgrade From Old) through this interface.
  • When right-clicking a process on the main window, a contextual menu allow to open, edit or iterate the processes.
  • Several BrainVISA can be launched by the same user without messing up the log files. Each BrainVISA instance now have its own session.
  • Processes and their parameters can be saved in a *.bvproc file. Opening this file in BrainVISA restore the process window.
  • There are so many other things that we truly regret that we did not update this changelog regularly.
  • Toolboxes

    T1 MRI:

    Tools for segmentation of various anatomical objects (hemispheres, grey matter, white matter, cortical sulci and gyri, etc.) from T1 weighted MRI.

    Sulci

    Diffusion and Tracking:

    Diffusion MR image analysis and fiber tracking.

  • New diffusion model added: QBall imaging.
  • Tracking can be don either with DTI model or QBall model.
  • New regularized probabilistic tracking methods.
  • Datamind:

    Cortical surface

    Structural analysis

    Biology

    Nuclear Imaging

    Morphometry

    TMS

    Data management

    Core BrainVISA toolbox. Contains processes for databases management: data importation, databases checking, update and exploration.

    Tools

    Core BrainVISA toolbox. Contains general processes that could not be put in another, more specific, toolbox.

    Version 3.0.2 (05/05/2006)

    General bug fixes:

  • Fixed a command not found error that prevented to use command lines programs from BrainVISA package (such as Aims... or Vip... commands) when BrainVISA was installed in a directory with space(s) in its name.
  • Diffusion and Fiber tracking:

  • During fiber tracking, the size of fascicles is limited to 20 000 points to avoid infinite loops in some cases.
  • Improvements

  • Documentation of a category (i.e. category_documentation.minf file) do not have to be in the main BrainVISA directory to be taken into account.
  • Version 3.0.1 (10/10/2005)

    Bug fixes:

  • Fixed a crash when using bundles features viewers
  • Log file is not expanded (therefore it is not read) at startup time. It avoids possible errors preventing BrainVISA to start when two BrainVISA instances are writing on the same cache file.
  • Fixed an error in DiskItem comparison operations
  • Changed the way system commands are run by BrainVisa on Mac and Windows. It seems to avoid hangups on Mac when BrainVisa is run from the desk or finder, and allows to stop processes on Windows.
  • The rotating icon animation when processes are running has been made more lightweight: it could cause severe slowdown on old and slow machines.
  • Diffusion and Fiber tracking:

  • Removed options related to bundles selection from fascicle tracking process
  • An error was fixed in linear interpolation of Aims library. This interpolation is used in several algorithms including diffusion and fiber tracking.
  • Improvements

  • Link with Matlab: multiple Matlab versions may now be supported. The matlab module in BrainVisa can switch between several pymat module compiled for either matlab 6 or 7. We have built pymat modules for both matlab versions in the binary packages (Linux, Windows, Mac, althrough they have not been tested at all on Mac)
  • Version 3.0.0 (29/06/2005)

    Well, the changelog hasn't been maintained for this version... There has been quite many changes, the most noticeable in the core of BrainVISA is a new pipeline system. 

    Version 2.3.5 (30/11/2004)

    Changes in the core:

  • Fix in combo boxes creation in database browser that broke compatibility with new Python-Qt binding library (SIP 4). This bug made the importation processes break on the Mac version, and probably the Windows version too.
  • Fix a possible crash in the redraw routines when a database browser combo was selected. Especially, this bug caused dirty crashes on the Mac version that made it quite unusable.
  • Version 2.3.4 (17/11/2004)

    Changes in the core:

  • Improvements in the installation program: it is not really part of BrainVisa, but there is no other place yet for it. Installation in directories containing space characters now work on all systems (esp. windows), running the SHFJEnvironmentVariables scripts is no longer necessary to run all Aims and Vip commands from a terminal, re-running the setup program is safe and may be used after moving the installation directory.
  • Changes to work with more recent versions of SIP/PyQt
  • Changes in processes:

  • SPM to AIMS normalization matrixes converter now also works with SPM2 normalization files
  • Version 2.3.2 (07/07/2004)

    Changes in the core:

  • Fixed an ambiguity in the standard database hierarchy that caused the anatomical pipeline to fail at the end (graphToTalairach)
  • Various fixes in C and C++ libraries used by BrainVisa processes. Amongst other things, this update should fix some problems on Windows XP (ROI graph writing, anatomical pipeline failure when using filenames containing space characters...)
  • GUI improvement in DiskItem finder box for data importation
  • ...
  • Changes in processes:

  • Fixes in SPM->AIMS transformation converter
  • SPM normalization/coregistration matrix converter, SPM images importation for anatomy, multiple cortical folds recognitions, ...
  • in anatomy/pipeline/PrepareSubject, the parameter allow_flip_initial_MRI has been set to false by default to avoid mistakes
  • Mesh smoothing process failed when filenames contained spaces
  • Version 2.3.0 (18/02/2004)

    Changes in the core:

  • Setup menus for options
  • Databases setup is done via the menus: editing options.py is no longer necessary.
  • Bug reports options
  • Better help system and french documentation. Ahem, er, yes, french. That's true...
  • Porting to Windows
  • Tooltips in processes GUI
  • A new process category: editors, are similar to viewers but are dedicated to data modification. For now, a "label image" editor calls the ROI edition tool of Anatomist
  • Lots of other things I don't remember
  • Changes in processes:

  • Diffusion and tracking pipeline
  • Anatomical pipeline:
  • Some cleanup has been done in the multiple processes of BrainVISA: the userLevels have been modified in some cases so as to show in basic level only really useful ones (pipelines etc).
  • Version 1.5 (23/05/2003)

    There was no changelog at his time.