= 3d Brain Atlas Reconstructor Installation (Ubuntu) =

----
**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(2-4,, inline)]]



== 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/register 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;
}}}

The 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.

Then follow instructions from `README` file to verify if the installation was successful.


== Installing required packages ==

=== Installation in Ubuntu 10.10 and Ubuntu 11.04 ===

  1. Install the Visualization Toolkit and other graphics libraries:
{{{
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
}}}
  2. Install python related packages:
{{{
sudo apt-get install \
python-gtkglext1 python-rsvg python-opengl python-numpy python-scipy python-wxgtk2.8
}}}
  3. Other packages:
{{{
sudo apt-get install \
potrace pstoedit python-setuptools python-epydoc
}}}

=== Installation in Kubuntu 11.10 ===

  1. Install the Visualization Toolkit and other graphics libraries:
{{{
sudo apt-get install \
libvtk5.6 libvtk5-dev libvtk5.6-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-wxgtk2.8
}}}
  3. Other packages:
{{{
sudo apt-get install \
potrace pstoedit python-setuptools python-epydoc
}}}

=== Installation in Ubuntu 10.04 ===

  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
}}}


=== 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 8.04 ===

Installation consists of following steps (just paste code blocks into terminal it should be fine:
  1. Installing Visualization Toolkit and other graphic libraries:
{{{
sudo apt-get install \
libvtk5 libvtk5-dev libvtk5-qt4 libvtk5-qt4-dev \
tk8.5 tk8.5-dev \
python-vtk libgtkgl2.0-1 libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti
}}}
  2. Installing python-related packages:
{{{
sudo apt-get install \
python-gtkglext1 python-opengl python-numpy python-scipy \
python-gnome2 python-gnome2-desktop python-gnome2-desktop-dev python-gnome2-dev python-wxgtk2.6
}}}
  3. Other packages:
{{{
sudo apt-get install \
potrace pstoedit python-setuptools subversion 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
}}}


== Troubleshooting ==
=== Segmentation fault in Ubuntu 11.10 ===
If the reconstructor crashes like that (numbers can vary):

{{{
$ ./3dbar.sh
./3dbar.sh: line 17:  2296 Segmentation fault      python bin/reconstructor/gui.py
}}}
  
the reason can be a bug in the 'python-vtk' package installed in your system.
Unfortunately there is no automated way to fix it - you have to do it manually:

1. Find a file named 'wxVTKRenderWindowInteractor.py'. It can be located
   in '/usr/share/pyshared/vtk/wx/' directory or in similar location:
 
{{{
$ find / -name 'wxVTKRenderWindowInteractor.py'
}}}

2. Edit the file with your favourite ASCII editor. In the example editor 'vim'
   is used and it is assumed that the path to the file is
   '/usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.py':
 
{{{
$ sudo vim /usr/share/pyshared/vtk/wx/wxVTKRenderWindowInteractor.py
}}}

3. Near 350th line of the file find a following line:
 
{{{
                d = '_%s_%s' % (d[2:], 'void_p')
}}}

4. Add '\0' characters to the line to make it like below:

{{{
                d = '_%s_%s\0' % (d[2:], 'void_p')
}}}

5. Save the modified file.


6. The bug should be fixed for now. Try running 3dBAR again. If this solution
   doesn't work - let us know.