//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//, //Ubuntu 10.04 LTS//, //Ubuntu 10.10// and //Ubuntu 11.04//. Installation on other Ubuntu versions or other Linux distributions is similar but the packages versions may be slightly different.
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[[PageOutline(2-3,, inline)]]

== Installing required packages ==


**Installation in Ubuntu 9.10**
  1. Install the Visualization Toolkit and other graphics 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
}}}
  2. Install python related packages:
{{{
sudo apt-get install \
python-gtkglext1 python-rsvg python-opengl python-numpy python-scipy python-wxgtk2.6
}}}
  3. Other packages:
{{{
sudo apt-get install \
potrace pstoedit python-setuptools python-epydoc
}}}

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

**Installation in Ubuntu 10.04**

Install the 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 python-epydoc
}}}

**Installation in Ubuntu 10.10 and Ubuntu 11.04**

Install the 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 python-epydoc
}}}

Once all the packages are installed it is time to create the directory structure.

== Getting the code ==
It is assumed that the main directory dedicated for 3dBAR is `/home/$USERNAME/3dbar`.
if you want to install it in another directory, replace `3dbar` with the desired path.


To get the latest stable version of 3dBAR fill out 
[http://service.3dbar.org/downloadForm the following form] then download 3dBAR using the link provided via email.

Unzip the file to your home directory and go to the 3dBAR directory:
{{{
mkdir ~/3dbar; unzip 3dbar_latest.zip -d ~/3dbar ; cd ~/3dbar;
}}}

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

Created directories have the following purposes:
  * **bin**: Holds all executable files, atlas parsers and auxiliary scripts
  * **lib**: Holds the 3dBAR api
  * **atlases**: Directory, where the source data, //CAF datasets// and reconstructed models are stored. Each dataset (denoted as DATASET_NAME) contains the following subdirectories:
    * atlases/DATASET_NAME/src : Here the source data is located. It can be placed manually by a user or downloaded from internet depending on a particular parser. 
    * atlases/DATASET_NAME/caf : This is the directory where a CAF dataset is generated by specific parsers.
    * atlases/DATASET_NAME/reconstructions : The directory for reconstructed models.

{{{#!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 ==
}}}