//How to install 3d Brain Atlas Reconstructor on Ubuntu?// = 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. ---- [[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 == }}}