BrainVISA/Anatomist FAQ
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BrainVISA/Anatomist FAQ |
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Before asking questions of reporting problems to the mailing lists, please make sure your question isn't answered here first. We have very few resources for technical support.
It depends on what you mean by free. Part of the software is free as in "free speech", and part of the software is free as in "free beer".
The CeCILL/GPL'd parts are enough to have a complete environment in which anyone
(or any lab) can plug their own processing tools. The data management (database-like
engine, graphics environment, data formats, I/O, and conversions) and visualization
(anatomist 3D renderings) are directly available.
The closed-source part is our implementation of some image processing
pipelines, and are not required to use the other parts. However without the
algorithms, the environment appears a bit empty, so they may be helpful after
all unless you have your own tools. They are available in binary format anyway:
we don't sell them, we don't make mony from them, and anyone can get and
use them.
See the download page.
See the download page for a list of supported systems.
The UNIX shell SHFJEnvironmentVariables scripts (sh and csh variants) are used to set
the path and other environment variables for the various programs of the SHFJ distribution.
As we compiled them on a given system without knowing about the target system the programs
will be running on, we have bundled with the pack a number of "system-wide" libraries,
such as Qt or the standard C++ library, which depend on the compiler and its
version. These libraries are suitable for running our software, but may conflict
with existing programs on your system.
These scripts are now internally called when running any command in the bin
directory of the package (brainvisa, anatomist, Aims or Vip commands...),
so you generally don't need to run them manually anymore (you had to in older 2.2.x packages).
However they can be useful to debug things in "real situation". Don't call them from your
personal config scripts (.profile, .cshrc or other). In 2.3 and later packages,
you just have to setup the PATH environment variable to reach the bin
directory of the package. This normally avoids any library conflict risks, but can still
cause the wrong programs to be called, especially python and qtconfig.
We have seen this problem on some Linux distributions (Mandrake 9.2) where no text
is displayed at all (not even little squares).
The problem is caused by incompatible antialiased fonts rendering libraries.
This problem can be fixed by providing a default font for Qt which doesn't use
FreeType or Xft. For now this is the only workaround we can suggest (except recompiling
everything).
This can be done using the qtconfig utility coming with Qt (and provided in our
packages). This utility enables to set the default look and font or all Qt applications,
these defaults will be saved in a $HOME/.qt/qtrc file on your
account.
The problem is that qtconfig itself would not display the texts
the first time you run it, so you would have to choose the font blindly
(this supposes you know where each button is!). On Linux you can use the
qtconfig of the system (not the one of the package).
Alternately you may edit (or create) the $HOME/.qt/qtrc file by
hand and provide a working default font in it, in the [General]
section, for instance:
[General] font=Lucida,12
BrainVISA needs Pymat
for Matlab interaction. Pymat is a python module written
in C++. Therefore it is compiled as a dynamic library file: pymatmodule.so.
When import pymat is used, Python tries to load pymatmodule.so.
Depending on Matlab verison, pymat may not load correctly: pymat in our package has been compiled for Matlab 6.5. It seems to work with any Matlab 6.x (?), but cannot work with Matlab 7.x because pymatmodule.so uses dynamic libraries provided by Mathwork and the symbols defined in these libraries have changed.
The solution is to compile pymat for your system. To make things easier, we have made a package with a makefile to build and install pymat in a already installed BrainVISA package. It can be dowloaded at the following address :
ftp://ftp.cea.fr/pub/dsv/anatomist/binary/pymat-brainvisa.tar.gz
To compile and install you must edit the makefile to select the appropriate directories according to your BrainVISA and Matlab installation and type the following command :
make install
In my lab, it works for both Matlab 6.1 and Matlab 6.5 under Linux. For other systems, I have not tested the solaris version yet and I do not have access to Matlab on Macintosh and Irix.
<SHFJ_pack_directory>/python/Lib/site-packagesrename the file:
pymat_disabled.dllto:
pymat.dllThat's all.
Yes. I don't care. Use XP (or best, Linux)
There are compilation instructions on this page, please read it and follow the instructions there first
Load "GLcore"
Load "glx"
If your 3D graphics card has linux support for accelerated rendering, you can also
load the dri module (see the DRI project):
Load "dri"Then restart your X server.
Well... please compile from sources...
Maybe its format is not recognized?
Anatomist is based on AIMS library, which has modular IO formats support.
Depending on how is built in the library, recognized volume formats are:
Vida, Dicom, Ecat, Jpeg and most other IO formats are now in plugins, this means they are external to the core Aims library, and loaded at run-time. If you can't use these formats, this may be due to the plugins loader not finding these plugins. Try running a command (anatomist for instance) with the option --info, and check the plugins and supported formats.
This is due to OpenGL. Maybe we could do something to display a pretty image for snapshot or printing, but it would be slower to display, and we have currently no time to work on it.
We think it's fixed in Anatomist 1.28. If it's not, tell us about
it please...
However destroying big objects with many children (graphs) still sometimes takes
an abnormally long time (not always, actually) - we have to debug it a bit more, one
day...
The problem is OpenGL windows don't display every triangle: half of them
are discarded and not shown. This seems to happen either on Linux and MacOSX
with Apple's X11 server, with some NVIDIA 3D cards like GeForce2, GeForce4,
Quadro4.
It is a bug in old Nvidia drivers/OpenGL, and it is fixed on recent drivers.
In our experience the problem happened with 3123 and 4191 versions of
Nvidia's linux (and Mac?) drivers: previous (2960) and next (4349 and later)
drivers are OK.
Yes. I don't care. Use XP (or best, Linux)
Everything is in the file options.py located in the directory $HOME/.brainvisa (if it exists) in your home directory. But in BrainVISA 1.6, you don't need to edit it manually anymore.
Brainvisa 1.6 (package release 2.3) includes a menu for graphical setup of the databases and some other options which should make you happy: options files do not need to be manually edited anymore (except for extreme wizard things).
LD_ASSUME_KERNEL=2.4.1
export LD_ASSUME_KERNEL
setenv LD_ASSUME_KERNEL 2.4.1
See the contacts page.