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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1. Installing required packages
2. Getting the code

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  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;

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.

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