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==================================== BRAINCARTA ====================================

STATUS:

 (alpha) ver 0.3.4.26 just migrated to SF.net

LICENSE:

 See file COPYING.

DESCRIPTION:

 We are planning to build Braincarta as a modern and flexible volumetric-data viewer tool. Using the powerful open source 3D visualization library VTK3D and the proven GUI platform Qt we are aiming at creating nice looking yet feature rich application.

 The project began as an in-house effort to provide state of the art volumetric visualizer up to the standards of modern hardware and open source software.




CORE-TEAM:

The core team, We, as of Feb 2011, consists of three people:

Dr. Nick Ramsey (www.nick-ramsey.eu) : initial design and idea; 

Dr. Bas Neggers (http://www.neuromri.nl/people/bas-neggers) : developer; MRI researcher; MRI data analyst

Petar Petrov (pip010 www.ppetrov.net) : main developer;





CONTRIBUTORS and CREDITS:

 * NA

 
 
DEVELOPMENT:

Why Python? While both VTK and Qt are native c++ libraries and indeed c++ might had been a better choice as far as performance goes, we find Python to give more benefits in general. First, Python is much easier to learn and adopt. It is free, open and already well accepted among researchers with vibrant community behind.

We recommend you use WingIDE 101, a free cross-OS Python IDE. It is the IDE used by the core team.

Here are the instruction on how to configure the developemt environment in Wing IDE 101 3.2.5, March 4 2010.

 1 - go to menu Edit->Config
 2 - fill the path the followin env-variables :

PYTHONPATH=/home/{your_user}/{your_vtk_build}/Wrapping/Python:/home/{your_user}/{your_vtk_build}/Wrapping/Python/vtk/qt4:/home/{your_user}/{your_vtk_build}/bin:/home/{your_user}/{your_Braincarta_SVN_workcopy}
LD_LIBRARY_PATH=/home/{your_user}/{your_vtk_build}/bin
 
Dev with PyQt : shell @ sudo apt-get install python-qt4 qt4-dev-tools python-qt4-dev build-essential pyqt4-dev-tools
 
 
 
INSTALATION:

Python is interpreted and we provide all the source. All you need to do is to run from the shell: python Braincarta.py

However!!! You need to insure the prerequisite libraries are installed on you system first and some system environments are set-up after. Please see PREREQUESITIES and DEPLOYMEMNT after.

Please!!! note that Braincarta is still in alpha version and we are not plannig an official setup /deploy application before a release candidate 1.0.

PREREQUISITIVE:

 * VTK 3D : from www.vtk.org Download and Build with Python wrappers enabled! Version 5.4.3 tested!

 * Qt/PyQt : most modern Linux distributions are coming with predeployed Qt, but that might not be the case with PyQt. Regardless of the case we recommend install these directly from repository. Latest version should suffice.
 
 * Python : needless to say!





DEPLOYMENT:

 * Linux (Ubuntu/Debian)

 After making sure you have installed Python,PyQt and succesfuly built VTK3D with Python wrappers enabeled.(Follow the general instruction to build VTK using CMake shell@cmake. or cmake.. ) hmm have to verify this eghh :(
 you need to open with editor your local profile paths, example : shell@gedit .profile
 then add the following lines to it, please reflect your local configuration {your_xxx} !!! , then save:
 
 PYTHONPATH=/home/{your_user}/{your_vtk_build}/Wrapping/Python:/home/{your_user}/{your_vtk_build}/bin
export PYTHONPATH

LD_LIBRARY_PATH=/home/{your_user}/{your_vtk_build}/bin
export LD_LIBRARY_PATH
 

 * OS-X

  TODO: howto: python, qt, pyqt, vtk
  [will do in March 2011] [instructions should be somehow similar to Linux]

 * Windows :

  Looking for !!!help!!!, someone who is willing to test builds on Microsoft Windows (WinXP, Vista,  Windows7). Since the development environment currently used is on Linux with WingsIDE and tested throughly on OS-X, Windows is down on the core team priority list.

Notes: 

hint about how to make installable deploy on mac-os and windows:
http://arstechnica.com/open-source/guides/2009/03/how-to-deploying-pyqt-applications-on-windows-and-mac-os-x.ars

http://tech.xster.net/tips/deploy-pyqt-applications-on-mac-os-x-with-pyinstaller/



USAGE:

The intended way to use Braincarta is to display fMRI activation maps along anatomical surface-mesh rendering of a human brain Gray Matter and Skin. All delivered in the form of nifti volumetric files. To produce a segmentation, a.k.a tissue classification, we use Matlab and the freely available SPM5 software package from http://www.fil.ion.ucl.ac.uk/spm/software/spm5/ . The hardware we use currently is PHILIPS Achieva 3T MRI.

Any other segmentation might work provided that : [TODO: Bas to explain]