BrainVISA ChangeLog

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:

• subject preparation now takes care of image orientations
• the pipeline also creates the head mesh

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.