#summary How to install 3d Brain Atlas Reconstructor on Ubuntu?

= 3d Brain Atlas Reconstructor Installation (Ubuntu) =

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*Note*: This procedure is valid for _Ubuntu 9.04_ and _Ubuntu 10.04 LTS_ and was tested on 4.08.2010.
For guides related to _Ubuntu 8.04_ see [InstallationUbuntu804  here]. 
Installation on other Ubuntu versions or other Linux distributions is simmilar, however not yet described.
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<wiki:toc max_depth="3" />

==Installing required packages==

Installation consists of following steps (just paste code blocks into terminal it should be fine (Ubuntu 9.10).
  # Installing Visualization Toolkit and other graphic libraries:
{{{
sudo apt-get install \
libvtk5.2 libvtk5-dev libvtk5.2-qt4 libvtk5-qt4-dev \
tk8.5 tk8.5-dev \
python-vtk libgtkgl2.0-1 libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti
}}}
  # Installing python-related packages:
{{{
sudo apt-get install \
python-gtkglext1 python-rsvg python-opengl python-numpy python-scipy python-wxgtk2.6
}}}
  # Other packages:
{{{
sudo apt-get install \
potrace pstoedit python-setuptools subversion python-epydoc
}}}

If You are developer, you may also want to install optional packages with documentation:
{{{
sudo apt-get install vtkdata vtk-doc vtk-examples
}}}

If you use Ubuntu 10.04 install following packages:
{{{
sudo apt-get install \
libvtk5.2 libvtk5-dev libvtk5.2-qt4 libvtk5-qt4-dev \
tk8.5 tk8.5-dev \
python-vtk libgtkgl2.0-1 libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti
}}}
{{{
sudo apt-get install \
python-gtkglext1 python-rsvg python-opengl python-numpy python-scipy python-wxgtk2.6
}}}
{{{
sudo apt-get install \
potrace pstoedit python-setuptools subversion python-epydoc
}}}

If you use Ubuntu 10.10 install following packages:
{{{
sudo apt-get install \
libvtk5.4 libvtk5-dev libvtk5.4-qt4 libvtk5-qt4-dev \
tk8.5 tk8.5-dev \
python-vtk libgtkgl2.0-1 libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti
}}}
{{{
sudo apt-get install \
python-gtkglext1 python-rsvg python-opengl python-numpy python-scipy python-wxgtk2.8
}}}
{{{
sudo apt-get install \
potrace pstoedit python-setuptools subversion python-epydoc
}}}

Once all packages are installed, it's time to create directory structure:
==Getting code==
It is assumed that main directory dedicated for software is `/home/$USERNAME/3dbar`.
if You want to install to another directory, please replace `3dbar` with desired path.

In order to get latest stable version use following command:
{{{
svn checkout http://3dbrainatlasreconstructor.googlecode.com/svn/tags/latest/ 
}}}

or get working code snapshot:
{{{
svn checkout http://3dbrainatlasreconstructor.googlecode.com/svn/trunk/ /home/$USERNAME/3dbar
}}}

then create directory where datasets will be stored:
{{{
mkdir -p /home/$USERNAME/3dbar/atlases
}}}

Created directories have following purposes:
  * *bin*: Holds all executable files, atlas parsers and auxiliary scripts
  * *lib*: Holds 3dBAR api
  * *atlases*: Directory, where source data, _CAF_ _datasets_ and reconstructed models are stored. Each dataset (denoted as DATASET_NAME) contains following subdirectories:
    * atlases/DATASET_NAME/src : Here source data is located. It may be put manually by user or ie. downloaded from internet depending on particular parser. 
    * atlases/DATASET_NAME/caf : Is the directory where CAF dataset is generated by particular parsers.
    * atlases/DATASET_NAME/reconstructions : Here performed reconstruction are generated using 3dBAR GUI.

<wiki:comment>
==Initial build==
In order create initial CAF datasets, generate documentation use following command in /home/$USERNAME/3dbar/ directory:
{{{
make -B -j N all
}}}

where N is number of parallel processes You want to use. If everything is installed correctly processing should be performed without any errors. Then 3dBAR GUI should be launched
{{{
./3dbar.sh
}}}
and used to perform reconstructions. If everything went fine, You may proceed to :


==Getting parsers for additional datasets==

</wiki:comment>